- GDR-LIST - Main Bioinformatics Lab

reminder: RosEXEC call for Nominations_deadline extended

by Dardick, Chris

Dear Rosaceae Community, The deadline for nominations has been extended to Friday, September 21st. We have 5 committee positions to fill and need 2 new international liaisons. We encourage anyone who has not participated before to consider serving on RosEXEC. By serving on RosEXEC you can help our research community remain competitive and it will provide you with excellent opportunities for building research collaborations. Candidates are welcome to nominate themselves. Please send nomination materials to Chris.dardick(a)ars.usd.gov<mailto:Chris.dardick@ars.usd.gov>. See attached for additional details. Call for nominations of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) The mission of the RosEXEC is to: * Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. * Define and promote research priorities based on input from the industry and research community. * Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni, and Jim McFerson) will be rotating off the RosEXEC in January of 2013. In Fall, 2012 five new RosEXEC members will be elected to a 3 year term starting January, 2013. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC including younger scientists and new faculty are encouraged. Industry representation is currently lacking and candidates from industry are also strongly encouraged. Members rotating off RosEXEC in January 2012 are not eligible for nomination (see list above). Members who will continue to serve in 2013 include, David Byrne, Thomas Chao, Bob Curtis, Sook Jung, Cameron Peace, Kate Evans, Mercy Olmstead, Janet Slovin, JD Swanson, Vance Whitaker, Jay Norelli, and Chris Dardick- so no need to nominate them as they will already be serving. Other former members of RosEXEC are eligible for nomination (see list below). We are also seeking nomination of 2 new international liaisons to a 2 year term on RosEXEC. International liaison members, Michela Troggio (EU) and Thomas Debener (EU) will be rotating off in January after 2 years of excellent service. Emily Buck (Australia/New Zealand) and Lee Meisel (S. America) will continue to serve in 2013. Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Chris Dardick (chris.dardick(a)ars.usda.gov<mailto:chris.dardick@ars.usda.gov>), Chair of the RosEXEC membership committee by September 15, 2011. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community wide election will be held in October. Former RosEXEC members: Bert Abbott, Abhaya Dandekar, Tom Davis, Amit Dhingra, Gennaro Fazio, Chad Finn, Stan Hokanson, Schuyler Korban, Kim Lewers, Jim Luby, Vladimir Shulaev, Dariusz Swietlik, Gary van Sickle, Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski, Phil Stewart and Gayle Volk. Former international liaisons: Pere Arús, Sue Gardiner, Jasper Rees, Dan Sargent, Herman Silva, David Chagné and Eric van de Weg. Chris Dardick USDA, ARS Appalachian Fruit Research Station 2217 Wiltshire Road Kearneysville, WV 25430 phone: 304-725-3451 ext. 387 fax: 304-728-2340 chris.dardick(a)ars.usda.gov<mailto:chris.dardick@ars.usda.gov> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

13 years, 5 months

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RosEXEC call for nominations

by Dardick, Chris

Call for nominations of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) The mission of the RosEXEC is to: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define and promote research priorities based on input from the industry and research community. · Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni, and Jim McFerson) will be rotating off the RosEXEC in January of 2013. In Fall, 2012 five new RosEXEC members will be elected to a 3 year term starting January, 2013. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC including younger scientists and new faculty are encouraged. Industry representation is currently lacking and candidates from industry are also strongly encouraged. Members rotating off RosEXEC in January 2012 are not eligible for nomination (see list above). Members who will continue to serve in 2013 include, David Byrne, Thomas Chao, Bob Curtis, Sook Jung, Cameron Peace, Kate Evans, Mercy Olmstead, Janet Slovin, JD Swanson, Vance Whitaker, Jay Norelli, and Chris Dardick- so no need to nominate them as they will already be serving. Other former members of RosEXEC are eligible for nomination (see list below). We are also seeking nomination of 2 new international liaisons to a 2 year term on RosEXEC. International liaison members, Michela Troggio (EU) and Thomas Debener (EU) will be rotating off in January after 2 years of excellent service. Emily Buck (Australia/New Zealand) and Lee Meisel (S. America) will continue to serve in 2013. Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Chris Dardick (chris.dardick(a)ars.usda.gov<mailto:chris.dardick@ars.usda.gov>), Chair of the RosEXEC membership committee by September 15, 2011. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community wide election will be held in October. Former RosEXEC members: Bert Abbott, Abhaya Dandekar, Tom Davis, Amit Dhingra, Gennaro Fazio, Chad Finn, Stan Hokanson, Schuyler Korban, Kim Lewers, Jim Luby, Vladimir Shulaev, Dariusz Swietlik, Gary van Sickle, Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski, Phil Stewart and Gayle Volk. Former international liaisons: Pere Arús, Sue Gardiner, Jasper Rees, Dan Sargent, Herman Silva, David Chagné and Eric van de Weg. Chris Dardick USDA, ARS Appalachian Fruit Research Station 2217 Wiltshire Road Kearneysville, WV 25430 phone: 304-725-3451 ext. 387 fax: 304-728-2340 chris.dardick(a)ars.usda.gov<mailto:chris.dardick@ars.usda.gov> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

13 years, 5 months

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RosEXEC AGENDA, July 31 8:00am at ASHS

by Norelli, Jay

Dear members of Rosaceae community, USRosEXEC will be meeting next week at the ASHS Annual Conference on Tuesday July 31, 2012 from 8:00-10:00 am in the Windsor Room of the InterContinental Hotel, Miami, Florida. If you will be attending ASHS, we hope to see you there. The meeting agenda is attached. During the meeting, Amy Iezzoni and Cameron Peace will discuss plans for the renewal of the USDA-NIFA-SCRI RosBREED project. You will also find attached a questionnaire they developed to solicit information from those in the Rosaceae community interested in participating in a 2nd RosBREED project. If you will not be attending the ASHS Annual Conference and would like to participate in the meeting via Skype, please contact JD Swanson (mailto:jd.swanson@salve.edu). Hope to see you next Tuesday, Jay Norelli 2012 Chair RosEXEC John (Jay) Norelli, Ph.D. Research Plant Pathologist USDA-ARS Appalachian Fruit Research Station 2217 Wiltshire Road Kearneysville, WV 25430 mailto:jay.norelli@ars.usda.gov (304) 725-3451 x264 FAX: (304) 728-2340 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

13 years, 6 months

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RGC6 registration is now open!

by Dan Sargent (EMR)

REGISTRATION IS NOW OPEN FOR THE SIXTH INTERNATIONAL ROSACEOUS GENOMICS CONFERENCE Registration for RGC6, the biennial focal point for the Rosaceae community, to be held in San Michele all’Adige, Italy between 30th September and 4th October 2012 is now open along with the submission of abstracts portal for both oral and poster presentations. Please see the conference website www.rgc6.org<http://www.rgc6.org> for information relating to the conference, accommodation, travel and social activities. If you require any additional information, please email info(a)rgc6.org<mailto:info@rgc6.org> We look forward to seeing you in Italy in the Fall! --East Malling Research registered office: New Road, East Malling, Kent ME19 6BJ. Tel. 01732-843833. Registered in England No. 5019373. Charity registration No.1102243. The information in this E-Mail and any attachments is confidential, may be legally privileged and is intended to be for the use of the intended recipient/s. If you are not the recipient named above please be aware that any disclosure, copying, distribution or use of the contents of this information is prohibited and may not represent the views of EMR. Activity and use of the East Malling Research E-mail system and any communications using it are monitored to secure its effective operation and for other lawful business purposes.

13 years, 8 months

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RGC6 - Sixth Rosaceous Genomics Conference - First Announcement

by Dan Sargent

*First Announcement - Sixth Rosaceous Genomics Conference* The Sixth Rosaceous Genomics Conference will be hosted by the Edmund Mach Foundation and will be held in San Michele all’Adige in the province of Trento, Italy between the 30th September 2012 and the 4th October 2012. The conference will be held at the PalaRotary wine cantina and conference centre and will bring together the entire Rosaceous Genomics community, as well as incorporating the Fall meetings of the RosExec and RosIGI. The first announcement has been posted on the official website for the conference: www.rgc6.org and information will be available soon regarding the the programme, registration, accommodation and travelling to/from the conference, as well as details about the social programme and planned events. If you require an invitation letter for your visa application for the conference, please visit the official website and use one of the methods of contacting us, so that we can assist in your application as soon as possible. Looking forward to seeing you in San Michele all'Adige! The RGC6 organising committee

14 years

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UC Davis 6K Peach SNPs available on GDR

by Main, Doreen

Approximately 6,000 peach SNPs were selected at UC Davis for two breeding populations: Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). These SNPs are now available for viewing in GBrowse as well as an Excel spreadsheet available on the peach genome project page<http://www.rosaceae.org/node/355>. Dorrie Main, PhD Associate Professor of Bioinformatics Dept. of Horticulture and landscape Architecture Washington State University 45 Johnson Hall Pullman, WA 99164-6414 Tel: 509-335-2774 (office) Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu><mailto:dorrie@wsu.edu> URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>

14 years

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Apple primary pseudo-haplotype assembly available on GDR

by Main, Doreen

The Malus x domestica genome v1.0 pseudo haplotype assemblies are a set of four different assemblies (primary and alternates 1, 2 and 3) derived from the contigs of the original v1.0 assembly. These pseudo haplotypes are intended to divde overlapping contigs in the original assembly into four different consensus sequences representing the four different haplotypes present in the apple genome. However, these assemblies are not true haplotypes, hence the name "pseudo haplotypes". Currently, only the primary pseudo haplotype assembly is available on GDR. Gaps of 200,000 N's were used to space scaffolds in the assembly. These pseudo haplotype assembles were constructed at the Instituo<http://www.iasma.it/> <http://www.iasma.it/> Agrario Di San Michelle <http://www.iasma.it/> All'Adige in collaboration with the NCBI<http://www.ncbi.nlm.nih.go/>. For more information, downloads and GBrowse visualization see the apple genome project page<http://www.rosaceae.org/projects/apple_genome>. Dorrie Main, PhD Associate Professor of Bioinformatics Dept. of Horticulture and landscape Architecture Washington State University 45 Johnson Hall Pullman, WA 99164-6414 Tel: 509-335-2774 (office) Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu><mailto:dorrie@wsu.edu> URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>

14 years

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PAG RosEXEC meeting Agenda

by Norelli, Jay

The U.S. Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) will be meeting at the PAG XX conference on Sunday, 15Jan in the Dover Meeting Room (not our usual location) from 8:00-10:00 am PST. It will be followed by a meeting of the Rosaceae International Genomics Initiative (RosIGI) from 10-noon. Both meetings are open to all who are interested in attending. An agenda for the RosEXEC meeting is attached. If you are interested in participating via skype, please email Chris Dardick (mailto:chris.dardick@ars.usda.gov) in case contact information changes. Hope to see you at PAG, Jay Norelli 2012 RosEXEC Chair John (Jay) Norelli Research Plant Pathologist USDA-ARS, Appalachian Fruit Research Station telephone: (304) 725-3451 x264 email: jay.norelli(a)ars.usda.gov<mailto:jay.norelli@ars.usda.gov> fax: (304) 728-2340 address: 2217 Wiltshire Road Kearneysville, WV 25430

14 years, 1 month

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Rosaceae Community

by Amy Iezzoni

Dear Rosaceae Community, I would like to invite you to a community discussion in San Diego sponsored by RosBREED. The goal of this discussion is to present an update on the informativeness of the 8K apple, 9K peach, and 6K cherry Illumina Infiinium SNP arrays and progress toward the development of a strawberry SNP array. The meeting is at 3:30 PST, Friday, January 13th, 2012 in the Courtyard Marriott San Diego Mission Valley (595 Hotel Circle South, San Diego) Inspire Ballroom. (Also see attached announcement.) We look forward to your joining us. Best wishes for a wonderful holiday season. Sincerely, Amy -- Amy Iezzoni Professor Michigan State University Department of Horticulture A342-B PSSB East Lansing, MI 48824 (517) 355 -5191 x 1391

14 years, 1 month

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LAST chance for RosEXEC Election

by Norelli, Jay

LAST chance to VOTE in RosEXEC 2012 Membership Election To cast your ballot go to: http://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_me… ALL US Rosaceae community members are eligible to vote. International members are eligible to vote for international liaisons. Polls will close Sunday, October 16, 2011 at midnight, Pacific ST. Detailed information below. VOTE Now<http://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_me…> RosEXEC Membership 2012 Ballot Announcement Five US RosEXEC committee members are rotating off the Committee this year: Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski and Phil Stewart Two international liaisons are rotating off: David Chagne and Herman Silva To replace these members, you are voting to elect five new U.S.-based members to serve 3 year terms and two international liaisons to serve 2 year terms on the RosEXEC committee. All US community members are eligible to vote. International members are eligible to vote for international liaisons. A brief bio and vision statement has been prepared by all candidates and is available at Candidate Bios<http://www.rosaceae.org/node/472>. Because the 2 continuing international liaisons are from Europe, to preserve a balance between European and non-European representation, the non-European candidate receiving the most votes and the remaining candidate with the most votes will be elected as international liaisons. There are a total of 16 elected U.S. members on RosEXEC, and we try to represent the diverse interests of the Rosaceae genomics, genetics, and breeding community. To preserve a balance between US members representing industry, academia and government representation, the industry candidate receiving the most votes and the four remaining candidates with the most votes will be elected as US members. The 11 continuing U.S. RosEXEC committee members are working in the following areas (under represented areas [<20%] are asterisked): Affiliation No. of members Supertribe Kerriodae (Prunus) 3.60 Pyrodae (Malus, Pyrus) 2.75 Rosodae 4.65 Institution Academia 8 Government 2* Industry 1*** U.S. Geographic Region East 3 South 6 West 2* Members who will continue to serve in 2012 :John Clark, Chris Dardick, Kate Evans, Kevin Folta, Ksenija Gasic, Amy Iezzoni, Jim McFerson, Jay Norelli, Mercy Olmstead, Janet Slovin, J.D. Swanson and Vance Whitaker John (Jay) Norelli Research Plant Pathologist USDA-ARS, Appalachian Fruit Research Station telephone: (304) 725-3451 x264 email: jay.norelli(a)ars.usda.gov<mailto:jay.norelli@ars.usda.gov> fax: (304) 728-2340 address: 2217 Wiltshire Road Kearneysville, WV 25430

14 years, 4 months

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VOTE NOW RosEXEC 2012 membership

by Norelli, Jay

VOTE NOW in RosEXEC 2012 Membership Election To cast your ballot go to: http://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_me… ALL US Rosaceae community members are eligible to vote. International members are eligible to vote for international liaisons. Polls will be open until October 7, 2011, detailed information below. VOTE Now<http://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_me…> RosEXEC Membership 2012 Ballot Announcement Five US RosEXEC committee members are rotating off the Committee this year: Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski and Phil Stewart Two international liaisons are rotating off: David Chagne and Herman Silva To replace these members, you are voting to elect five new U.S.-based members to serve 3 year terms and two international liaisons to serve 2 year terms on the RosEXEC committee. All US community members are eligible to vote. International members are eligible to vote for international liaisons. A brief bio and vision statement has been prepared by all candidates and is available at Candidate Bios<http://www.rosaceae.org/node/472>. Because the 2 continuing international liaisons are from Europe, to preserve a balance between European and non-European representation, the non-European candidate receiving the most votes and the remaining candidate with the most votes will be elected as international liaisons. There are a total of 16 elected U.S. members on RosEXEC, and we try to represent the diverse interests of the Rosaceae genomics, genetics, and breeding community. To preserve a balance between US members representing industry, academia and government representation, the industry candidate receiving the most votes and the four remaining candidates with the most votes will be elected as US members. The 11 continuing U.S. RosEXEC committee members are working in the following areas (under represented areas [<20%] are asterisked): Affiliation No. of members Supertribe Kerriodae (Prunus) 3.60 Pyrodae (Malus, Pyrus) 2.75 Rosodae 4.65 Institution Academia 8 Government 2* Industry 1*** U.S. Geographic Region East 3 South 6 West 2* Members who will continue to serve in 2012 :John Clark, Chris Dardick, Kate Evans, Kevin Folta, Ksenija Gasic, Amy Iezzoni, Jim McFerson, Jay Norelli, Mercy Olmstead, Janet Slovin, J.D. Swanson and Vance Whitaker

14 years, 5 months

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My email address has been hacked

by 苑 Z. Yuan

各位朋友大家好，很抱歉，我的邮箱被人黑客，并发出不健康的网站链接，请勿打开链接！ Hi,everyone, I am so sorry. My email adrress has been hacked and sent some bad website links to my contacts. Please donn't open them. 顺祝安好！苑兆和，博士，研究员山东省果树研究所/山东省农业科学院山东省泰安市龙潭路64号，271000 Best regards, Zhaohe Yuan, PhD, Professor Shandong Institute of Pomology, 64 Longtan Rd., Tai'an, Shandong Province, China, 271000 手机（Cell）： 86-13953817188 (in China) 办公（Office）： 86-538-8334070 (in China) 传真(Fax)： 86-538-8266350（in China） Email: zhyuan88@hotmail.com，zhyuan88@gmail.com

14 years, 5 months

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(no subject)

by 苑 Z. Yuan

http://www.r2sol.com/wp-includes/frkigfj.htm

14 years, 6 months

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RosEXEC nominations extended to August 26

by Norelli, Jay

The call for nominations to RosEXEC has been extended until August 26, 2011. If you are interested in serving on the RosEXEC you can nominate yourself. See instructions below. Call for nominations of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) The mission of the RosEXEC is to: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define and promote research priorities based on input from the industry and research community. · Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski and Phil Stewart) will be rotating off the RosEXEC in January of 2012. In 2011, five new RosEXEC members will be elected to a 3 year term to replace them in January. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members rotating off RosEXEC in January 2012 are not eligible for nomination (see list above). Members who will continue to serve in 2012 include, John Clark, Chris Dardick, Kate Evans, Kevin Folta, Ksenija Gasic, Amy Iezzoni, Jim McFerson, Jay Norelli, Mercy Olmstead, Janet Slovin, J.D. Swanson and Vance Whitaker , so no need to nominate them as they will already be serving. Other former members of RosEXEC are eligible for nomination. International liaison members, Herman Silva (South America) and David Chagné (Australia/New Zealand) will be rotating off in January after 2 years of excellent service and we are also seeking nomination of international liaisons to a 2 year term on RosEXEC. Liaison members remaining through 2013 are Thomas Debener (Europe) and Michela Troggio (Europe). Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Jay Norelli (jay.norelli(a)ars.usda.gov <file:///C:\Documents%20and%20Settings\jnorelli\My%20Documents\Administration\Rosaceae%20Community\RosEXEC%20officer\Election2011\jay.norelli@ars.usda.gov> ), Chair of the RosEXEC membership committee by August 15, 2011. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community wide election will be held in September. Former RosEXEC members: Herb Aldwinckle, Bert Abbott, Abhaya Dandekar, Tom Davis, Amit Dhingra, Gennaro Fazio, Chad Finn, Stan Hokanson, Schuyler Korban, Kim Lewers, Jim Luby, Cameron Peace, Vladimir Shulaev, Dariusz Swietlik, Gary van Sickle, and Gayle Volk. Former international liaisons: Pere Arús, Sue Gardiner, Jasper Rees, Dan Sargent, and Eric van de Weg. Jay Norelli Chair of RosEXEC membership committee John (Jay) Norelli Research Plant Pathologist USDA-ARS, Appalachian Fruit Research Station telephone: (304) 725-3451 x264 email: jay.norelli(a)ars.usda.gov <mailto:jay.norelli@ars.usda.gov> fax: (304) 728-2340 address: 2217 Wiltshire Road Kearneysville, WV 25430

14 years, 6 months

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RosEXEC call for nominations

by Norelli, Jay

Call for nominations of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) The mission of the RosEXEC is to: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define and promote research priorities based on input from the industry and research community. · Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (Angela Baldo, Nahla Bassil, Jim Hancock, Bryon Sosinski and Phil Stewart) will be rotating off the RosEXEC in January of 2012. In 2011, five new RosEXEC members will be elected to a 3 year term to replace them in January. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members rotating off RosEXEC in January 2012 are not eligible for nomination (see list above). Members who will continue to serve in 2012 include, John Clark, Chris Dardick, Kate Evans, Kevin Folta, Ksenija Gasic, Amy Iezzoni, Jim McFerson, Jay Norelli, Mercy Olmstead, Janet Slovin, J.D. Swanson and Vance Whitaker, so no need to nominate them as they will already be serving. Other former members of RosEXEC are eligible for nomination. International liaison members, Herman Silva (South America) and David Chagné (Australia/New Zealand) will be rotating off in January after 2 years of excellent service and we are also seeking nomination of international liaisons to a 2 year term on RosEXEC. Liaison members remaining through 2013 are Thomas Debener (Europe) and Michela Troggio (Europe). Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Jay Norelli (jay.norelli(a)ars.usda.gov), Chair of the RosEXEC membership committee by August 15, 2011. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community wide election will be held in September. Former RosEXEC members: Herb Aldwinckle, Bert Abbott, Abhaya Dandekar, Tom Davis, Amit Dhingra, Gennaro Fazio, Chad Finn, Stan Hokanson, Schuyler Korban, Kim Lewers, Jim Luby, Cameron Peace, Vladimir Shulaev, Dariusz Swietlik, Gary van Sickle, and Gayle Volk. Former international liaisons: Pere Arús, Sue Gardiner, Jasper Rees, Dan Sargent, and Eric van de Weg. John (Jay) Norelli Research Plant Pathologist USDA-ARS, Appalachian Fruit Research Station telephone: (304) 725-3451 x264 email: jay.norelli(a)ars.usda.gov <mailto:jay.norelli@ars.usda.gov> fax: (304) 728-2340 address: 2217 Wiltshire Road Kearneysville, WV 25430

14 years, 7 months

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Rosaceae unigene analysis

by Main, Doreen

Hi Folks, We are planning to generate new unigene data sets for Rosaceae genera and would like to be able to include next generation transcript data in the unigene data sets. Some of you have already provided your assembled data and we will include those in the next builds (unigene v5) with acknowledgement of who generated the data sets and what tissues/development stage etc were included. Please let me know if you have any datasets you would like included by the end of March as we will begin the process at the beginning of April. In terms of the annotation we will provide the following for the unigene sequences. GO Terms, InterPro Scan domains, KEGG, Swissprot, TrEMBL annotation, relevant plant protein homologs which will be searchable, browsable and downloadable (with all summary statistics) Mapping of the unigenes to the peach, apple and strawberry genomes (excel file linked to GBrowse and a GBrowse track) Identification of microsatellites and COS markers (also available as downloadable file and linked to GBrowse). Thanks Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 10 months

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RosEXEC meeting Sun 16 Jan

by Jim McFerson

Our annual meeting is set for the same time and place as customary, in conjunction with the PAG Conference, San Diego: Sun 8-10am Towne Room, Town & Country Center I will be sending out an agenda shortly. All Community members are welcome. Jim ##### James R. McFerson, PhD WA Tree Fruit Research Commission 1719 Springwater Ave Wenatchee, WA 98801 off: 509-665-8271 mob: 509-669-3900

15 years, 1 month

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Plant Phenotypes Workshop PAG XIX

by Mary Schaeffer

Dear Colleague, If you are attending PAG XIX, San Diego this year, I invite you to attend the PAG Plant Phenotypes Workshop Sunday Jan 16 8-10:10 am Pacific Salon 1, and also to visit Exhibit Booth #427 PAG XIX Outreach Consortium for Plant Genome Data Resources. At the WORKSHOP, there will be a panel discussion about phenotype data resources. Towards that end, we would greatly appreciate if you would spend 10-15 minutes to take a survey of your data needs. https://www.surveymonkey.com/s/PlantPhenotypeWorkshop2011 Workshop program: 8:00 Welcome >>> >>> Featured talks (in order) >>> >>> 8:10 Sean May "If you build it.....(NASC phenomics)" >>> >>> 8:30 Matt Vaughn "iPlant's cyberinfrastructure for high-throughput image >>> analysis" >>> >>> 8:50 Richard Poire "Next generation plant biofuel research and the High >>> Resolution Plant Phenomics Centre" >>> >>> 9:10 Geoff Fincher "Evaluation of next generation phenotyping: the >>> Australian Plant Phenomics Facility" >>> >>> UPDATES, Wrap-up and discussion >>> >>> 9:30 Laurel Cooper "Plant Ontology" >>> >>> 9:35 Elizabeth Arnoud "Crop Ontology update" >>> >>> 9:40 Eva Huala "RCN Phenotype Ontology Plants, animals, etc." >>> >>> 9:45 Chi-Ren Shyu "Next generation phenotype data mining update" and >>> wrap-up/survey discussion. >>> 9:50-10:10 Panel Discussion and community input We are looking forward to meeting you. >>> >>> >>> Best regards, >>> >>> >>> Mary Schaeffer and Chi-Ren Shyu, Co-Organizers of Plant Phenotype >>> Workshop at PAG 2011 >>>

15 years, 1 month

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LAST DAY FOR rosEXEC VOTING

by Jim McFerson

Go to the GDR and follow the link to elect your U.S. RosEXEC!!! http://www.rosaceae.org Voting ends TODAY 19 Nov 2010 You are voting for individuals to serve for a three-year term on the U.S. Genomics, Genetics, and Breeding Executive Committee (RosEXEC). There are five open seats on the 15 member Committee and 2 open seats for international liaisons. Check out the candidate bios and RosEXEC vision statements. Vote for candidates to represent the diversity of our fabulous family. Any individual working in Rosaceae is eligible to vote, including students. Non-U.S. community members are urged to vote for their international liaisons. Questions? Contact Jim McFerson (mcferson(a)treefruitresearch.com), Chair of the RosEXEC membership committee.

15 years, 2 months

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GDR Emai list

by Verma, Sujeet

My email address is - sujeet.verma(a)email.wsu.edu Sujeet Verma Ph.D Candidate Tree Fruit Genetics and Genomics Department of Horticulture and LA Lab: 509-335-5298, Office: FSHN 322 (509-335-0543) Washington State University, Pullman, USA

15 years, 3 months

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my email

by oron gar

My email: Oron.gar(a)mail.huji.ac.il Oron Gar PhD. student The Hebrew university of Jerusalem The Robert H. Smith Faculty of Agriculture, Food and Environment The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture Professor Dani Zamir Laboratory P.O Box 12, Rehovot 76100 Israel Tel: 972-52-5676460, 972-8-9489250 Fax: 972-8-948-9943 E-MAIL: ORON.GAR(a)MAIL.HUJI.AC.IL P Please consider the environment before printing this email or its attachments

15 years, 3 months

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(no subject)

by mickael malnoy

my e mail malnoym(a)gmail.com -- Mickael MALNOY PhD Research and Innovation Center Structural and Functional Genomics Fondazione Edmund Mach (FEM) Istituto Agrario San Michele (IASMA) Via Mach 1, 38010 San Michele all'Adige (TN) Italy Phone office: +39 0461 61 55 36 Phone lab: +39 0461 61 54 16 Fax: +39 0461 65 09 56 Website: www.fondazioneedmundmach.eu E-mail: mickael.malnoy(a)iasma.it

15 years, 3 months

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Two weeks to vote for RosEXEC

by Jim McFerson

Community Members: Many of you have already voted for new members to RosEXEC. Be aware that voting will terminate on 19 Nov, two weeks from now. Please visit the GDR web site to cast your ballot electronically. http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_rosexec_memb ership_2011_vote_form.cgi&style=height:1600px;width:950px All community members are eligible to vote. Thanks! Jim ##### James R. McFerson, PhD WA Tree Fruit Research Commission & Vice-Chair, RosEXEC 1719 Springwater St Wenatchee, WA 98801 work: 509.665.8271 x1 mob: 509.669.3900

15 years, 3 months

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RosEXEC ELECTIONS UNDERWAY

by Jim McFerson

Rosaceae Community Member: We are ready to vote on the 2011 candidates for RosEXEC. Voting begins 26 Oct and ends 19 Nov. Please go to the following web site to learn about the candidates¹ background and vision for RosEXEC. Then submit your electronic ballot. http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_rosexec_memb ership_2011_vote_form.cgi&style=height:1600px;width:940px The community will elect five new U.S. members and two new International members to a 3-year term. U.S.-based members will vote for both U.S. candidates and International candidates. International community members will vote for International candidates only. This year¹s slate is diverse. We encourage you to consider voting to create a leadership group that will appropriately represent the amazing diversity of the Rosaceae community. Current RosEXEC membership can be found at [http://www.rosaceae.org/node/291] As a reminder, the mission of RosEXEC is to: · Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. Thanks again to the following U.S. and International members rotating off: U.S. International Chris Dardick David Chagné Amit Dhingra Jasper Rees Jim Luby Eric van de Weg Cameron Peace Gayle Volk QUESTIONS? Please contact Jim McFerson (mcferson(a)treefruitresearch.com), Chair, RosEXEC membership committee. VOTE EARLY!

15 years, 3 months

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SNP Summit deadline tommorow 5 pm PDT

by Main, Doreen

Hi Folks, The deadline to register is 5 pm PDT Friday October 22. Thanks Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 3 months

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Reminder: SNP Summit Registration

by Main, Doreen

Hi Folks, If you are planning on attending the SNP summit in South Africa on November 13 and 14, can you please register using the form on GDR. http://www.rosaceae.org/node/375 Thanks Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 3 months

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LAST DAY FOR ROSEXEC NOMINATIONS

by Jim McFerson

LAST DAY TO NOMINATE CANDIDATES FOR ROSEXEC!!! EXTENDED NOMINATION DEADLINE 15 Oct 2010 We are seeking nominations of individuals to serve for a three-year term on the U.S. Genomics, Genetics, and Breeding Executive Committee (RosEXEC). There are five open seats on the 15 member Committee and 2 open seats for international liaisons. While we do have six individuals nominated already, we would like to receive at least another six nominations. Please consider nominating a colleague you believe would contribute to supporting the mission of RosEXEC: · Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2010 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa), Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagne (Aus/NZ). Two new members are needed to serve two year terms and we are seeking at least one to be in Europe. Prior to nomination, the nominator is required to contact the nominee and confirm willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Send nominations to Jim McFerson (mcferson(a)treefruitresearch.com), Chair of the RosEXEC membership committee, by 15 Oct 2010. Nominees will then be contacted by the membership committee and asked to provide a brief bio and vision statement. The community-wide election will be managed by the Genome Database for the Rosaceae (GDR) and held via internet from 25 Oct-19 Nov 2010. The next meeting of RosEXEC will be on 16 Jan 2011 in conjunction with the PAG Conference, San Diego CA.

15 years, 4 months

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apple genome sequence and annotation available on GDR

by Main, Doreen

The apple genome sequence and associated annotation are now available in GDR. Many thanks to Riccardo Velasco and his team for providing the data. While there are links in the text below, please go to the GDR home page (www.rosaceae.org) to access the data as the email links sometimes get re-routed incorrectly via the mail server at WSU. Apple Genome v1.0 General Information * From this site you can browse and download the whole genome sequence of the Velaso et al., 2010 published apple genome assembly v1.0; predicted gene transcripts, their locations and putative function based on homology to known genes. You can BLAST your sequences against the genome sequence, the predicted genes and associated transcripts. You can search and browse the chromosomes, predicted genes and markers in GBrowse and view the evidence for each prediction and feature. Important Details About This Assembly * Because of the heterozygous nature of the Malus x domestica genome, pseudomolecules corresponding to the chromosomes are not presented. To preserve haplotype information, this assembly consists of sets of assembled contigs organized into metacontigs (clusters) and anchored to the chromosomes using 1,643 genetic markers. There is no consensus sequence from assembled contigs. Please see the whole genome <http://www.rosaceae.org/projects/apple_genome#publication> publication in Nature Genetics for further details. * Chromosomes are labeled 'chr1' through 'chr17' for each of the 17 chromosomes respectively. Contigs from different haplotypes may align and overlap on the same chromosomal region. Metacontigs that could not be anchored have been arranged sequentially in a chromosome-like feature named 'unanchored', however, the order of metacontigs on this "chromosome" is arbitrary. * Visualization of the genome using GBrowse <http://www.rosaceae.org/gb/gbrowse/malus_x_domestica> orients the contigs within a chromosome, however, gene predictions, location of markers, tRNA and protein alignments were constructed and aligned using contig sequences. * 5' and 3' UTR regions are currently not available for gene models. Data and Tools * Apple Genome Sequence * View the Apple v1.0 genome assembly and annotations in GBrowse <http://www.rosaceae.org/gb/gbrowse/malus_x_domestica> * Download the Malus x domestica genome contigs <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 278 MB compressed) * Download the Malus x domestica chloroplast sequence <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ch…> (fasta, 50 KB compressed) * Download the Malus x domestica mitochondrial sequence <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.mi…> (fasta, 126KB compressed) * Apple Genome Sequence Predicted Genes * Download the predicted consensus gene set CDS sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 18 MB compressed) * Download the predicted consensus gene set peptides sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 12 MB compressed) * Download other gene prediction CDS sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ot…> (fasta, 78 MB compressed) * Download other gene prediction peptides sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ot…> (fasta, 49 MB compressed) * Predicted Gene Function * Download the non-redundant, best-match predicted protein homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 59 MB) * Download species/database specific protein homologs: * 71,657 apple gene peptides with Arabidopsis homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 78 MB) * 71,245 apple gene peptides with Swiss-Prot homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 54 MB) * 84,380 apple gene peptides with TrEMBL homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 68 MB) * 73,479 apple gene peptides with Grape homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 62 MB) * 78,017 apple gene peptides with Peach homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 66 MB) * 79,527 apple gene peptides with Poplar homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 69 MB) * BLAST your sequences * using the GDR NCBI BLAST Server <http://www.rosaceae.org/bio/content?title=&url=http://app.bioinfo.wsu.edu/b…;> - results returned to your screen * using the GDR BATCH BLAST Server <http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_blast> - upload many sequences and have the results parsed out in an excel file * Markers * Download the apple markers with links to GBrowse & CMAP <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ma…> * Questions or Comments? * Contact us with questions/feedback/comments (select the apple genome in the dropdown box in the contact form <http://www.rosaceae.org/contact> ) * Whole Genome Publication * Riccardo Velasco , Andrey Zharkikh , Jason Affourtit , Amit Dhingra , Alessandro Cestaro , Ananth Kalyanaraman , Paolo Fontana , Satish K Bhatnagar , Michela Troggio , Dmitry Pruss , Silvio Salvi , Massimo Pindo , Paolo Baldi , Sara Castelletti , Marina Cavaiuolo , Giuseppina Coppola , Fabrizio Costa , Valentina Cova , Antonio Dal Ri , Vadim Goremykin , Matteo Komjanc , Sara Longhi , Pierluigi Magnago , Giulia Malacarne , Mickael Malnoy , Diego Micheletti , Marco Moretto , Michele Perazzolli , Azeddine Si-Ammour , Silvia Vezzulli , Elena Zini , Glenn Eldredge , Lisa M Fitzgerald , Natalia Gutin , Jerry Lanchbury , Teresita Macalma , Jeff T Mitchell , Julia Reid , Bryan Wardell , Chinnappa Kodira , Zhoutao Chen , Brian Desany , Faheem Niazi , Melinda Palmer , Tyson Koepke , Derick Jiwan begin_of_the_skype_highlighting end_of_the_skype_highlighting , Scott Schaeffer, Vandhana Krishnan , Changjun Wu , Vu T Chu , Stephen T King , Jessica Vick , Quanzhou Tao , Amy Mraz , Aimee Stormo , Keith Stormo , Robert Bogden , Davide Ederle , Alessandra Stella , Alberto Vecchietti , Martin M Kater , Simona Masiero , Pauline Lasserre , Yves Lespinasse , Andrew C Allan , Vincent Bus , David Chagné , Ross N Crowhurst , Andrew P Gleave , Enrico Lavezzo , Jeffrey A Fawcett , Sebastian Proost , Pierre Rouzé , Lieven Sterck , Stefano Toppo , Barbara Lazzari , Roger P Hellens , Charles-Eric Durel , Alexander Gutin , Roger E Bumgarner , Susan E Gardiner , Mark Skolnick , Michael Egholm , Yves Van de Peer , Francesco Salamini & Roberto Viola. The Genome of the Domesticated Apple (Malus x domestica Borkh.) <http://dev.rosaceae.org/bio/content/?title=&url=http://www.rosaceae.org/cgi…;> Nature Genetics 42, 833-839. 2010. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 4 months

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RosEXEC Nominations extended

by Main, Doreen

EXTENDED NOMINATION DEADLINE 15 Oct 2010 We are seeking nominations of individuals to serve for a three-year term on the U.S. Genomics, Genetics, and Breeding Executive Committee (RosEXEC). There are five open seats on the 15 member Committee and 2 open seats for international liaisons. While we do have six individuals nominated already, we would like to receive at least another six nominations. Please consider nominating a colleague you believe would contribute to supporting the mission of RosEXEC: * *****Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community. * *****Define research priorities based on input from the industry and research community. * *****Facilitate scientific interaction and foster dynamic research teams. * *****Promote research priorities. * *****Coordinate educational efforts from the research community to the industry and the public. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2010 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa), Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagne (Aus/NZ). Two new members are needed to serve two year terms and we are seeking at least one to be in Europe. Prior to nomination, the nominator is required to contact the nominee and confirm willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Send nominations to Jim McFerson (mcferson(a)treefruitresearch.com), Chair of the RosEXEC membership committee, by 15 Oct 2010. Nominees will then be contacted by the membership committee and asked to provide a brief bio and vision statement. The community-wide election will be managed by the Genome Database for the Rosaceae (GDR) and held via internet from 25 Oct-19 Nov 2010. The next meeting of RosEXEC will be on 16 Jan 2011 in conjunction with the PAG Conference, San Diego CA. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 4 months

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Italian-led international research consortium decodes the apple genome

by Main, Doreen

The apple genome was today published by the Italian-led international consortium. Please find attached their press release. Congratulations to all concerned for this important work. The GDR team have the genome data and we hope to release it very soon on GDR. We will send out another email when it is available on GDR. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 5 months

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RGC5 Oral Submissions due date next Monday

by Main, Doreen

________________________________ From: Jasper Rees [mailto:reesj@arc.agric.za] Sent: Fri 8/13/2010 3:23 AM To: Main, Doreen Subject: RGC5 Oral Submissions due date next Monday Hi Dorrie, can you post this on the gdr-list please? To remind people that we have a due date for oral abstracts for RGC5 that is coming up on Monday! Many thanks! j --- Dr D Jasper G Rees Tel +27 12 529 9101/9106 Head: Biotechnology Platform Cell +27 82 415 9295 Agricultural Research Council FAX +27 12 565 4667 Private Bag X05 Skype: jasperrees Onderstepoort, 0110 Email: ReesJ(a)arc.agric.za South Africa

15 years, 6 months

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RCG5 student funding support enquiry

by Main, Doreen

Dear US Based Rosaceae Researchers, We would like to compile a list of potential student applicants who would like to attend RCG5 if they had some financial support. If you have any students who fit this category and would present a poster or talk, could you send us the following information about them so we can submit it to the NSF in support of our application for funding. NAME of STUDENT: GENDER: ETHNICITY: ORGANISATION: AREA of RESEARCH: SUPERVISOR NAME: Many Thanks Dorrie Main and Bryon Sosinski Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 6 months

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Call for nominations to US RosEXEC

by Norelli, Jay

Call for nomination of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC): The mission of the RosEXEC is to: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (Chris Dardick, Amit Dhingra, Jim Luby, Cameron Peace and Gayle Volk) are rotating off the RosEXEC committee in January 2011. In 2010, five new RosEXEC members will be elected to a 3 year term to replace them in January 2011. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2011 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa) and Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagné (Aus/NZ). Two new members are needed to serve two year terms where we are seeking at least one to be in Europe. Please nominate candidates to serve as international liaisons and confirm their interest before submitting your nominations, as described below. Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Jim McFerson (mcferson(a)treefruitresearch.com <mailto:mcferson@treefruitresearch.com> ) Chair of the RosEXEC membership committee, and/or Jay Norelli (jay.norelli(a)ars.usda.gov <file:///C:\Documents%20and%20Settings\jnorelli\My%20Documents\Administration\Rosaceae%20Community\RosEXEC%20officer\July%208%20meeting\jay.norelli@ars.usda.gov> ) RosEXEC Secretary, by September 1, 2010. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community-wide election will be held in November.

15 years, 6 months

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Rosaceae SNP Summit Information

by Main, Doreen

A Rosaceae community SNP Summit will be held at the Wallenberg Centre, Stellenbosch University in Stellenbosch, Cape Town, South Africa, on the 13th and 14th of November 2010. This will be immediately prior to the 5th International Rosaceae Genomics Conference to be held on the 14-17th of November 2010 at the same location. At the SNP Summit, hosted by the USDA NIFA funded RosBREED project (www.rosbreed.org <http://www.rosbreed.org/> ), RosBREED participants and other interested community members will decide on the best SNP genotyping platform to conduct genome scans within Rosaceae (apple, peach, cherry and strawberry) and select the sequences to be included on the platform. If you are interested in attending the SNP summit, please contact Dorrie Main (RosBREED Genomics Team Leader at dorrie(a)bioinfo.wsu.edu <mailto:dorrie@bioinfo.wsu.edu> . For more information on the RosBREED project, see www.rosbreed.org <http://www.rosbreed.org/> For more information on RGC5, see http://www.rgc5.co.za/ <http://www.rgc5.co.za/> Best Regards Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 7 months

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Announcing 5th International Rosaceae Genomics Conference in Cape Town SA, Nov 14-17, 2010

by Main, Doreen

RCG5 willl be held November 14-17, 2010 in Cape Town , South Africa. For full conference details, see the RCG5 website at http://www.rgc5.co.za <http://www.rgc5.co.za> Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

15 years, 7 months

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Peach Genome Release

by randalls＠bioinfo.wsu.edu

Hi Folks, Great news! The International Peach Genome Initiative (IPGA) has released version 1.0 of the peach genome sequence. Peach v1.0 currently consists of 8 pseudomolecules (the first 8 scaffolds) representing the 8 chromosomes of peach and are numbered according to their corresponding linkage groups (a total of 202 scaffolds were generated). The genome sequencing consisted of approximately 7.7 fold whole genome shotgun sequencing employing the accurate Sanger methodology, and was assembled using Arachne. The assembled peach scaffolds (total of 202) cover nearly 99% of the peach genome, with over 92% having confirmed orientation. To further validate the quality of the assembly, 74,757 Prunus ESTs were queried against the genome at 90% identity and 85% coverage, and we found that only ~2% were missing. This is truly a high quality genome! Gene prediction and annotation, is an ongoing process that may take years to complete, but current estimates indicate that peach has 28,689 transcripts and 27,852 genes. Peach v1.0 was generated from DNA from the doubled haploid cultivar 'Lovell' which means that the genes and intervening DNA is "fixed" or identical for all alleles and both chromosomal copies of the genome. This doubled haploid nature was confirmed by the evaluation of >200 SSRs, and has facilitated a highly accurate and consistent and assembly of the peach genome. For more information about the project and access to the peach genome data and tools go GDR(www.rosaceae.org/peach/genome/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.rosaceae.o…> ), JGI (www.phytozome.org/peach/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.phytozome.…> ) or the Istituto di Genomica Applicata (http://services.appliedgenomics.org/gbrowse/prunus_public/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://services.appli…> ) Cheers The IPGA folks p.s. please note that GDR is now located at www.rosaceae.org <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=https://mail.cahnrs.w…> , you will be redirected from the old GDR site to the new one. We will be sending out a newsletter about GDR very soon. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/> Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory

15 years, 10 months

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test

by randalls＠bioinfo.wsu.edu

Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory

15 years, 10 months

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Reminder of Wednesday deadline for voting for RosEXEC membership

by Dorrie Main

Dear US Based Rosaceae Genomics and Genetics Community, Thank you for nominating candidates to serve as RosEXEC and International Liaison Members. To vote on new members please go to http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2010_vote_for… and vote for 5 RosEXEC members and 2 International Liaison members. For more information on RosEXEC see http://www.bioinfo.wsu.edu/gdr/community/rosexec/index.php If you have any problems voting please email me at dorrie(a)wsu.edu or dorrie.main(a)gmail.wsu.edu Please note voting must be completed by 5pm PST on Wednesday January 6th. Many thanks Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu/gdr

16 years, 1 month

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RosEXEC Membership Voting

by Dorrie Main

Dear US Based Rosaceae Genomics and Genetics Community, Thank you for nominating candidates to serve as RosEXEC and International Liaison Members. To vote on new members please go to http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2010_vote_for… and vote for 5 RosEXEC members and 2 International Liaison members. For more information on RosEXEC see http://www.bioinfo.wsu.edu/gdr/community/rosexec/index.php If you have any problems voting please email me at dorrie(a)wsu.edu or dorrie.main(a)gmail.wsu.edu Please note voting must be completed by 5pm PST on Wednesday January 6th. Many thanks Wishing you all the best in 2010. Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu/gdr

16 years, 1 month

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Positions announcement in Sustainable Agriculture at University of New Hampshire

by Main, Doreen

The University of New Hampshire is advertising a cluster hire (seven positions!) in the areas of Sustainable Agriculture and Ecosystems Science. At least four of these positions have direct relevance to horticultural crops. Please see attached document for more details.

16 years, 2 months

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RosBREED BIMS post-doc position available

by Main, Doreen

Hi Folks, Please forward this postition description to anyone you think might be interested in this position. We are seeking a cadre of tomorrow's leaders to join our team on an exciting new "science to the marketplace" federally funded project. "RosBREED: Enabling Marker-Assisted Breeding in Rosaceae" is a four-year trans-disciplinary project focused on rosaceous crops (apple, cherry, peach, and strawberry) involving 12 U.S. research institutions, international collaborators, and private sector participants. RosBREED aims to identify crucial fruit breeding selection targets and efficient selection strategies, including a software-based pipeline for utilizing genomics and socio-economics knowledge for efficient delivery of new cultivars with superior fruit quality. Recruited team members will regularly interact with scientists and stakeholders across institutions and countries to achieve RosBREED goals. BIMS Developer Position We are seeking a post-doctoral associate to lead the development of breeding decision aid tools, databases, and other information management software aimed for the plant breeding community. The incumbent will interact closely and regularly with U.S. Rosaceae breeding programs to identify needs, gaps, and strengths of current breeding information management practices, and work with a programmer to synthesize a state-of-the-art Breeding Information Management System (BIMS) that is interoperable with genomic databases, statistical analysis packages, and able to match and surpass the needs of the Rosaceae breeding community. A strong background in quantitative genetics and great communication skills are required, and experience with plant breeding is highly desirable. The position is based on the Washington State University Campus in beautiful Pullman, WA and has a duration of 3-4 years (see www.rosbreed.org <http://www.rosbreed.org> ) Contact Dr. Cameron Peace cpeace(a)wsu.edu <mailto:cpeace@wsu.edu> or Dr. Gennaro Fazio gf35(a)cornell.edu <mailto:gf35@cornell.edu> for further information. Gennaro Fazio, PhD Apple Rootstock Breeder and Geneticist Plant Genetic Resources Unit USDA ARS Cornell University - 630 W. North St., Geneva, NY 14456 (315) 787-2480 Office (315) 787-2216 Fax

16 years, 2 months

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Roexec Membership Nomination Extended-Friday, Dec 4- Maloideae and Industry reps needed

by Bassil, Nahla

Dear US Based Rosaceae Genomics and Genetics Community, I would like to thank all community members who nominated candidates for RosEXEC. The list of nominees obtained so far does not have a single Maloideae or industry candidate. Therefore, the RosEXEC Membership subcommittee is extending nominations until Friday Dec 4th to give you the opportunity to nominate Maloideae members and industry members. Please make sure to please confirm with the prospective candidates that they are willing to be nominated and potentially serve before you submit them as candidates to me. A copy of the previous letter is pasted below. Thank you, Nahla Bassil, Chair, RosEXEC Membership Committee Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 nahla.bassil(a)ars.usda.gov It is time to nominate the 2010 USRosEXEC members. After three/four years of excellent service the following US members are rotating off the RosEXEC committee: * Albert Abbott (Amygdaloideae, Univ, S), * Chad Finn (Rosoideae, ARS, W), * Abhaya Dandekar (Maloideae, Amygdaloideae Univ, W) * Schuyler Korban (Maloideae, Univ, E) * Gennaro Fazio (Maloideae, ARS, E) The committee thus loses: * 1 Rosoideae, 2.5 Maloideae and 1.5 Amygdaloideae crop focus representatives; * 3 university and 2 ARS representatives; * 2 eastern location (E), 2 western location and 1 southern (S) location representatives. Members who will continue to serve in 2009 include Nahla Bassil, Chris Dardick, Amit Dhingra, Jim Luby, Gayle Volk, Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart and Cameron Peace, so no need to nominate them as they will already be serving. To help maintain a balanced committee, we are asking you to nominate, by email, research and industry community members of whom one should have a major focus on Rosoideae, two on Maloideae and two on Amygdaloideae. Individuals with mixed focus can also be nominated. Please take this into account when you nominate candidates and please confirm with the prospective candidates that they are willing to be nominated and potentially serve before you submit them as candidates to Nahla. International liason member rotating off this year include Sue Gardiner (Aus/NZ), Herman Silva (South Americ) and Dan Sargeant (Europe). Remaining members through 2010 are Jasper Rees (Africa) and Eric van de Weg (Europe). Two new members are needed to serve two year terms where we are seeking at least one to be outside of Europe. Please nominate candidates and again confirm their interest before submitting your nominations. US Rosaceae Genomics, Genetics and Breeding community members may nominate as many candidates as you wish at this stage by sending a list of the nominees to membership chair, Nahla Bassil at nahla.bassil(a)ars.usda.gov. You have until November 20th to nominate candidates. Following these nominations, we will compile a candidate list for the actual vote via a webform. If you have any questions please contact Nahla Bassil at the aforementioned email address. Many thanks Nahla Bassil Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 nahla.bassil(a)ars.usda.gov

16 years, 2 months

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RosEXEC Membership Nominations-2010-Ends November 20

by Bassil, Nahla

Thank you to the members who nominated new members and a quick reminder that the deadline for new nominations is Friday November 20th. Dear US Based Rosaceae Genomics and Genetics Community, It is time to nominate the 2010 USRosEXEC and International Liaison Members. After three/four years of excellent service the following US members are rotating off the RosEXEC committee: * Albert Abbott (Amygdaloideae, Univ, S), * Chad Finn (Rosoideae, ARS, W), * Abhaya Dandekar (Maloideae, Amygdaloideae Univ, W) * Schuyler Korban (Maloideae, Univ, E) * Gennaro Fazio (Maloideae, ARS, E) The committee thus loses: * 1 Rosoideae, 2.5 Maloideae and 1.5 Amygdaloideae crop focus representatives; * 3 university and 2 ARS representatives; * 2 eastern location (E), 2 western location and 1 southern (S) location representatives. Members who will continue to serve in 2009 include Nahla Bassil, Chris Dardick, Amit Dhingra, Jim Luby, Gayle Volk, Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart and Cameron Peace, so no need to nominate them as they will already be serving. To help maintain a balanced committee, we are asking you to nominate, by email, research and industry community members of whom one should have a major focus on Rosoideae, two on Maloideae and two on Amygdaloideae. Individuals with mixed focus can also be nominated. Please take this into account when you nominate candidates and please confirm with the prospective candidates that they are willing to be nominated and potentially serve before you submit them as candidates to Nahla. International liaison members rotating off this year include Sue Gardiner (Aus/NZ), Herman Silva (South America) and Dan Sargent (Europe). Remaining members through 2010 are Jasper Rees (Africa) and Eric van de Weg (Europe). Two new members are needed to serve two year terms where we are seeking at least one to be outside of Europe. Please nominate candidates and again confirm their interest before submitting your nominations. US Rosaceae Genomics, Genetics and Breeding community members may nominate as many candidates as you wish at this stage by sending a list of the nominees to membership chair, Nahla Bassil at nahla.bassil(a)ars.usda.gov. You have until November 20th to nominate candidates. Following these nominations, we will compile a candidate list for the actual vote via a webform. If you have any questions please contact Nahla Bassil at the aforementioned email address. Many thanks, Nahla Bassil Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 nahla.bassil(a)ars.usda.gov

16 years, 3 months

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RosEXEC Membership Nominations-2010

by Bassil, Nahla

Dear US Based Rosaceae Genomics and Genetics Community, It is time to nominate the 2010 USRosEXEC and International Liaison Members. After three/four years of excellent service the following US members are rotating off the RosEXEC committee: * Albert Abbott (Amygdaloideae, Univ, S), * Chad Finn (Rosoideae, ARS, W), * Abhaya Dandekar (Maloideae, Amygdaloideae Univ, W) * Schuyler Korban (Maloideae, Univ, E) * Gennaro Fazio (Maloideae, ARS, E) The committee thus loses: * 1 Rosoideae, 2.5 Maloideae and 1.5 Amygdaloideae crop focus representatives; * 3 university and 2 ARS representatives; * 2 eastern location (E), 2 western location and 1 southern (S) location representatives. Members who will continue to serve in 2009 include Nahla Bassil, Chris Dardick, Amit Dhingra, Jim Luby, Gayle Volk, Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart and Cameron Peace, so no need to nominate them as they will already be serving. To help maintain a balanced committee, we are asking you to nominate, by email, research and industry community members of whom one should have a major focus on Rosoideae, two on Maloideae and two on Amygdaloideae. Individuals with mixed focus can also be nominated. Please take this into account when you nominate candidates and please confirm with the prospective candidates that they are willing to be nominated and potentially serve before you submit them as candidates to Nahla. International liaison members rotating off this year include Sue Gardiner (Aus/NZ), Herman Silva (South America) and Dan Sargent (Europe). Remaining members through 2010 are Jasper Rees (Africa) and Eric van de Weg (Europe). Two new members are needed to serve two year terms where we are seeking at least one to be outside of Europe. Please nominate candidates and again confirm their interest before submitting your nominations. US Rosaceae Genomics, Genetics and Breeding community members may nominate as many candidates as you wish at this stage by sending a list of the nominees to membership chair, Nahla Bassil at nahla.bassil(a)ars.usda.gov. You have until November 20th to nominate candidates. Following these nominations, we will compile a candidate list for the actual vote via a webform. If you have any questions please contact Nahla Bassil at the aforementioned email address. Many thanks, Nahla Bassil Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 nahla.bassil(a)ars.usda.gov

16 years, 3 months

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FW: Research Associate (Post Doc) at Oregon State Univ.

by Main, Doreen

________________________________ From: Pankaj Jaiswal (OSU) [mailto:jaiswalp@science.oregonstate.edu] Sent: Wed 7/15/2009 11:27 AM To: Main, Doreen Subject: Research Associate (Post Doc) at Oregon State Univ. Please post to the GDR list. Thanks Pankaj Position Title: Research Associate (Post Doc) The Department of Botany and Plant Pathology has an immediate opening for a Research Associate (Post Doc) to work on a cereal plant genome wide gene expression analysis. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in Dr. Pankaj Jaiswal's lab (http://www.science.oregonstate.edu/bpp/). How to Apply: To review the position description and apply, go to posting #0004455 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). For full consideration, apply by 07/31/09 when review of applications will begin. This position is required to develop a comprehensive gene expression catalog of rice and other cereal plant genes in various the plant development stages. The project includes histological studies, whole genome transcriptome and proteome data generation and analysis. The incumbent will be responsible for designing microarray and whole genome transcriptome/digital gene expression experiment(s) using newer high throughput sequencing technologies developed by Illumina, 454-LifeSciences, etc. Development of methods suitable to the experimental conditions and plant material being investigated, carrying out the experiments on analysis of anatomical samples using microscopy and whole genome transcriptome, data analysis and publication of the results in peer reviewed journals and submission to major data repositories. Besides this, the incumbent will also participate in lab's outreach activities, help in mentoring undergraduates and graduate students. Successful candidate will work with existing lab personnel and various collaborators that includes project PIs, faculty, highly trained PhD. level bioinformatics specialists, software developers and the department's fellow postdoc and graduate students. Required qualifications: - PhD in Plant Biology, Molecular Biology, Genetics, Biochemistry, Biological Chemistry, Metabolomics, or related field. - Worked previously on gene expression data generation and analysis in their PhD studies or postdoctoral training. Demonstrated expertise in studying plant development, anatomy, histology, microarrays, gene expression, proteomics, genetics and general understanding of plant biochemistry and gene regulation. - Demonstrated ability for independent and critical thinking, excellent communication skills in oral and written presentations in English and ability to work in teams. Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA

16 years, 7 months

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FW: 2009 Molecular Markers in Horticulture Symposium Announcement

by Bassil, Nahla

Having trouble viewing this email? Click here <http://campaign.constantcontact.com/render?v=0012IbiHsnbTWuzaIuobUoYoEo U7i3Xkipi_BwrIBYQgRNzhKLYDRmmRH6r034t8Fh-rKNwNBnSVmuCMIjYqTs5gpCpS7qNeXZ T2p_a9qNS_IGypt9FQvkBIw%3D%3D> You're receiving this email because of your relationship with Oregon State University Conference Services. Please confirm <http://visitor.constantcontact.com/c.jsp?t=1102621007632.8693.38463381. 2&m=1101658764278&wl=F> your continued interest in receiving email from us. You may unsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8 mJyceMGyAvUerctgjqPhAfy3xnkrpK8H_uh7y-U-EHLTOeuRpaohfG9AKrtap-qvyA%3D%3D > if you no longer wish to receive our emails. <http://rs6.net/on.jsp?t=1102621007632.0.1101658764278.8693&ts=S0396&o=h ttp://ui.constantcontact.com/images/p1x1.gif> Click to visit our website! <http://rs6.net/tn.jsp?et=1102621007632&s=8693&e=001-DnWwS50VCZRVsLa8I1s zZBd-WUbuOpTHMfEFHxrvE33yd_sGjyhkzOT83Jcy93nSNX9SsYULRUxfaLR5RYpUfZqYePc 6to_AXM5kF8g5r18z8eHG8jNHOy7gm_tDzAofvmsq-r2aHuS2x20bb1t8EnGCDlEjXJp> UPDATES! Dealine for Manuscript submissions extended to THURSDAY July 2, 2009 Please register for the Post Conference and Companion tours at: http://secure.oregonstate.edu/ocs/register.php?event=377 The final program for the oral presentations is now available at the website: http://oregonstate.edu/conferences/molecularmarkers2009 The deadline for Hotel reservations at the Conference rate has been extended to July 7, 2009. MAKE YOUR RESERVATIONS NOW! Follow the link on the conference website This symposium is organized by the ISHS, USDA-ARS and OSU Sponsors for Molecular Markers in Horticulture 2009<http://oregonstate.edu/conferences/molecularmarkers2009/sponsors.jp g> OSU Conference Services | 200 LaSells Stewart Center | Corvallis, OR 97331 Tel: (541) 737-9300 conferences(a)oregonstate.edu <mailto:%20conferences@oregonstate.edu> Fax: (541) 737-9315 Forward email <http://ui.constantcontact.com/sa/fwtf.jsp?m=1101658764278&ea=nahla.bass il%40ars.usda.gov&a=1102621007632> Safe Unsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8 mJyceMGyAvUerctgjqPhAfy3xnkrpK8H_uh7y-U-EHLTOeuRpaohfG9AKrtap-qvyA%3D%3D > This email was sent to nahla.bassil(a)ars.usda.gov by conferences(a)oregonstate.edu. Update Profile/Email Address <http://visitor.constantcontact.com/d.jsp?p=oo&v=001ytzJgXCdPi4OJiECzQd8 mJyceMGyAvUerctgjqPhAfy3xnkrpK8H_uh7y-U-EHLTOeuRpaohfG9AKrtap-qvyA%3D%3D > | Instant removal with SafeUnsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8 mJyceMGyAvUerctgjqPhAfy3xnkrpK8H_uh7y-U-EHLTOeuRpaohfG9AKrtap-qvyA%3D%3D > (tm) | Privacy Policy <http://ui.constantcontact.com/roving/CCPrivacyPolicy.jsp> . Email Marketing <http://www.constantcontact.com/index.jsp?cc=custom01> by <http://www.constantcontact.com/index.jsp?cc=custom01> Oregon State University Conference Services | OSU Conference Services | 100 LaSells Stewart Center | Corvallis | OR | 97331

16 years, 7 months

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Abstract Deadline-May 1- Blueberry SSRs

by Main, Doreen

Subject: [Hort-All] 2009 Molecular Markers in Horticulture Symposium 4thAnnouncement <http://rs6.net/tn.jsp?et=1102556298233&s=9324&e=001YnVzJ9VNYstWuHoFoLvgvo9B…> Fourth Announcement Abstract Submission Deadline Extended: May 1st Deadline for early registration: 20 April, 2009 Late registration fees are incurred after April 20th. If you need a Letter of Invitation for your visa application, please contact: Wambui Njuguna njugunaw(a)onid.orst.edu <mailto:njugunaw@onid.orst.edu> A draft of the program is available at http://oregonstate.edu/conferences/molecularmarkers2009 <http://rs6.net/tn.jsp?et=1102556298233&s=9324&e=001YnVzJ9VNYstWuHoFoLvgvo9B…> Please join us! On behalf of the Biotechnology Commission of the International Society for Horticultural Sciences (ISHS), the convener and local organizing committee invite you to participate in a symposium devoted to Molecular Markers in Horticulture. The symposium will be held July 29 to August 1, 2009 at the Alumni Center located on the Oregon State University (OSU) campus in Corvallis, Oregon. Program Information: You are invited to submit papers on DNA-based markers, applications of next-generation sequencing and analytical tools and bioinformatics as they pertain to horticultural crops. You will tour the OSU CGRB Core Laboratory which provides services in genomics, functional genomics, biocomputing and bioinformatics and the USDA ARS Corvallis Genebank <http://rs6.net/tn.jsp?et=1102556298233&s=9324&e=001YnVzJ9VNYstw_BEM7bRgvh_E…> where molecular markers are used for managing world collections of hazelnut, pear and many berry crops. During the symposium, you will have an opportunity to explore the state of molecular marker science in 5 sections: 1. Plant Germplasm Identification and Characterization 2. Marker-assisted Breeding 3. Molecular Markers in Phylogenetics and Evolution 4. Analytical Approaches and Bioinformatics 5. Applications of Next-Generation Sequencing Important Deadlines April 20, 2009 April 20, 2009 May 1, 2009 June 5, 2009 June 25, 2009 June 25, 2009 Early Registration Ends Abstracts due to Scientific Committee Author notifications if accepted, oral/poster Manuscripts due for publication in Acta Horticulturae Hotel reservations due Registration for post-conference tour closes Location: You will enjoy the mild summer temperatures in Western Oregon moderated by the nearby Pacific Ocean, the beautiful coniferous forests in the adjacent Coast and Cascade mountain ranges, and you will sample the award-winning wines from local small vineyards and the abundant seasonal vegetables, fruits and berries. *Limited financial assistance may become available. Please check the request assistance box on the registration form to be placed on a waiting list for financial assistance. This symposium is organized by the ISHS, USDA-ARS and OSU Sponsors for Molecular Markers in Horticulture 2009 OSU Conference Services | 200 LaSells Stewart Center | Corvallis, OR 97331 Tel: (541) 737-9300 conferences(a)oregonstate.edu <mailto:%20conferences@oregonstate.edu> Fax: (541) 737-9315 Forward email <http://ui.constantcontact.com/sa/fwtf.jsp?m=1101658764278&ea=hort-all%40hor…> Safe Unsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8mOqh…> This email was sent to hort-all(a)hort.oregonstate.edu by conferences(a)oregonstate.edu. Update Profile/Email Address <http://visitor.constantcontact.com/d.jsp?p=oo&v=001ytzJgXCdPi4OJiECzQd8mOqh…> | Instant removal with SafeUnsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8mOqh…> (tm) | Privacy Policy <http://ui.constantcontact.com/roving/CCPrivacyPolicy.jsp> . Email Marketing <http://www.constantcontact.com/index.jsp?cc=custom01> by <http://www.constantcontact.com/index.jsp?cc=custom01> Oregon State University Conference Services | OSU Conference Services | 100 LaSells Stewart Center | Corvallis | OR | 97331

16 years, 9 months

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Reminder to Register for Molecular Markers in Horticulture Symposium 2009

by Main, Doreen

________________________________ From: Nahla Basil [mailto:conferences@oregonstate.edu] Sent: Mon 4/13/2009 11:22 AM To: Main, Doreen Subject: Reminder to Register for Molecular Markers in Horticulture Symposium 2009 REMINDER Deadline for registration and abstract submission: 20 April, 2009 If you need a Letter of Invitation for your visa application, please contact: Wambui Njuguna njugunaw(a)onid.orst.edu A draft of the program with keynote speakers for each section is now available. Visit the Symposium website:http://oregonstate.edu/conferences/molecularmarkers2009 <http://rs6.net/tn.jsp?et=1102549237474&s=9322&e=0017ExMIkBxgwG5e4eblnSgQ0Sm…> Looking forward to see you at this timely and exciting symposium, Best regards, Nahla Bassil, Convener Plant Molecular Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 bassiln(a)hort.oregonstate.edu nahla.bassil(a)ars.usda.gov On behalf of the Biotechnology Commission of the International Society for Horticultural Sciences (ISHS), the convener and local organizing committee invite you to participate in a symposium devoted to Molecular Markers in Horticulture. The symposium will be held July 29 to August 1, 2009 at the Alumni Center located on the Oregon State University (OSU) campus in Corvallis, Oregon. Program Information: IYou are invited to submit papers on DNA-based markers, applications of next-generation sequencing and analytical tools and bioinformatics as they pertain to horticultural crops. You will tour the OSU's CGRB Core Laboratories <http://rs6.net/tn.jsp?et=1102549237474&s=9322&e=0017ExMIkBxgwFcghpPI9zU2FXa…> which provides services in genomics, functional genomics, biocomputing and bioinformatics and the USDA ARS Corvallis genebank <http://rs6.net/tn.jsp?et=1102549237474&s=9322&e=0017ExMIkBxgwHozEl6hzI1wQEu…> where molecular markers are used for managing world collections of hazelnut, pear and many berry crops. During the symposium, you will have an opportunity to explore the state of molecular marker science in 5 sections: 1. Plant Germplasm Identification and Characterization 2. Marker-assisted Breeding 3. Molecular Markers in Phylogenetics and Evolution 4. Analytical Approaches and Bioinformatics 5. Applications of Next-Generation Sequencing Important Deadlines April 20, 2009 April 20, 2009 May 1, 2009 June 5, 2009 June 25, 2009 June 25, 2009 Early Registration Ends Abstracts due to Scientific Committee Author notifications if accepted, oral/poster Manuscripts due for publication in Acta Horticulturae Hotel reservations due Registration for post-conference tour closes *Limited financial assistance may become available. Please check the request assistance box on the registration form to be placed on a waiting list for financial assistance. Location: You will enjoy the mild summer temperatures in Western Oregon moderated by the nearby Pacific Ocean, the beautiful coniferous forests in the adjacent Coast and Cascade mountain ranges, and you will sample the award-winning wines from local small vineyards and the abundant seasonal vegetables, fruits and berries. This symposium is organized by the ISHS, USDA-ARS and OSU Sponsors for Molecular Markers in Horticulture 2009 OSU Conference Services | 200 LaSells Stewart Center | Corvallis, OR 97331 Tel: (541) 737-9300 conferences(a)oregonstate.edu <mailto:%20conferences@oregonstate.edu> Fax: (541) 737-9315 Forward email <http://ui.constantcontact.com/sa/fwtf.jsp?m=1101658764278&ea=dorrie%40wsu.e…> Safe Unsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8mBt0…> This email was sent to dorrie(a)wsu.edu by conferences(a)oregonstate.edu. Update Profile/Email Address <http://visitor.constantcontact.com/d.jsp?p=oo&v=001ytzJgXCdPi4OJiECzQd8mBt0…> | Instant removal with SafeUnsubscribe <http://visitor.constantcontact.com/d.jsp?p=un&v=001ytzJgXCdPi4OJiECzQd8mBt0…> (tm) | Privacy Policy <http://ui.constantcontact.com/roving/CCPrivacyPolicy.jsp> . Email Marketing <http://www.constantcontact.com/index.jsp?cc=custom01> by <http://www.constantcontact.com/index.jsp?cc=custom01> Oregon State University Conference Services | OSU Conference Services | 200 LaSells Stewart Center | Corvallis | OR | 97331

16 years, 10 months

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Re: [GDR] RosBREED M-TA table update

by Nnadozie Oraguzie

Got it. Many thanks. Nnadozie -----Original Message----- From: Charles-Eric Durel [mailto:Charles-Eric.Durel@angers.inra.fr] Sent: Monday, March 09, 2009 1:40 AM To: Nnadozie Oraguzie Cc: gdr-list(a)bioinfo.wsu.edu Subject: Re: [GDR] RosBREED M-TA table update Hi Nnadozie, Another paper on apple : fire blight resistance QTL in wild/ornamental Malus. Best regards, CE Nnadozie Oraguzie a écrit : > > Hi folks, > > Its that time of the year again for SCRI grant proposals! We would > like to update the Rosaceae marker-trait association (M-TA) table > prepared last year for the RoseBREED proposal. We are particularly > interested in any new QTLs, major gene loci, genes and linked markers > that may have been discovered and probably published since the last > table was created. Please provide the information using the format in > the last table which you will find at the following links: > > Full information: > http://www.hrt.msu.edu/faculty/Iezzoni/Links/TABLE%20of%20M-T%20associations %20for%20website_Sept2008.pdf > > > Summary Table: > http://www.hrt.msu.edu/faculty/Iezzoni/Links/Summary%20Table%20of%20MT%20Ass ociations.pdf > > That is, the information should follow the sequence: species, trait, > QTL, major trait locus, genes (including LGs for genes/major loci and > LGs, LOD score, percentage of variation explained for QTLs), > source/population, linked markers, references, use in MAPS (i.e., > marker-assisted parent selection) and MASS (marker-assisted seedling > selection). I would appreciate if you could include the full citation > details for all references in the full information table. Please send > the information to me by the 25^th of March 2009. > > Thank you so much for your assistance. > > Nnadozie > > Nnadozie Oraguzie > > Associate Professor > > Prunus Breeding, Genetics & Genomics > > Department of Horticulture & Landscape Architecture > > Washington State University-IAREC > > 24106 N Bunn Road Prosser > > WA 99350 USA > > Tel: 1 509 786 9271 > > Fax: 1 509 786 9370 > > E-mail:noraguzie@wsu.edu > > ------------------------------------------------------------------------ > > _______________________________________________ > Main Bioinformatics Laboratory > GDR-LIST mailing list > GDR-LIST(a)mail.bioinfo.wsu.edu

16 years, 11 months

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Re: [GDR] RosBREED M-TA table update

by Nnadozie Oraguzie

Hi folks, It's that time of the year again for SCRI grant proposals! We would like to update the Rosaceae marker-trait association (M-TA) table prepared last year for the RoseBREED proposal. We are particularly interested in any new QTLs, major gene loci, genes and linked markers that may have been discovered and probably published since the last table was created. Please provide the information using the format in the last table which you will find at the following links: Full information: http://www.hrt.msu.edu/faculty/Iezzoni/Links/TABLE%20of%20M-T%20associations %20for%20website_Sept2008.pdf Summary Table: http://www.hrt.msu.edu/faculty/Iezzoni/Links/Summary%20Table%20of%20MT%20Ass ociations.pdf That is, the information should follow the sequence: species, trait, QTL, major trait locus, genes (including LGs for genes/major loci and LGs, LOD score, percentage of variation explained for QTLs), source/population, linked markers, references, use in MAPS (i.e., marker-assisted parent selection) and MASS (marker-assisted seedling selection). I would appreciate if you could include the full citation details for all references in the full information table. Please send the information to me by the 25th of March 2009. Thank you so much for your assistance. Nnadozie Nnadozie Oraguzie Associate Professor Prunus Breeding, Genetics & Genomics Department of Horticulture & Landscape Architecture Washington State University-IAREC 24106 N Bunn Road Prosser WA 99350 USA Tel: 1 509 786 9271 Fax: 1 509 786 9370 E-mail:noraguzie@wsu.edu

16 years, 11 months

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remove email

by Neil Nagata

Please remove me

16 years, 11 months

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Postdoctoral Fellow and Software Developer Positions in Comparative Genomics and Systems Biology

by Pankaj Jaiswal

Postdoctoral Fellow and Software developer positions in Comparative Genomics and Systems Biology Jaiswal lab at Oregon State University (http://www.oregonstste.edu) is seeking talented and motivated candidates for current and future job openings as postdoctoral fellows and software developers in the systems biology and bioinformatics. The successful candidates are expected to have either or both the experience of working in a biology wet lab and/or bioinformatics, computational biology lab. The successful candidate(s) will collaborate with researchers from Biochemistry, Molecular Biology, Plant Development, Genetics and Systems Biology programs. Postdoctoral applicants must have a Ph.D. (or equivalent degree) in biology, bioinformatics, molecular biology, biochemistry, genetics, computational biology or related fields, and some demonstrated experience in computer science/bioinformatics. For the computational biologists and software developer positions in addition to their experience and interest in biology, expertise in at least one scientific programming language and relational data management system is preferred. Candidates with experience in network analysis methods are encouraged to apply. Candidates with BS/MS degrees are also encouraged to apply for future positions in the lab. Interested individuals should send or email letter of intent/cover letter , CV/Resume with contact info of three references, and a 1-2 page description of previous accomplishments to the following address. E mail is preferred. Pankaj Jaiswal, Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Email: jaiswalp(a)science.oregonstate.edu -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org

17 years, 3 months

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Post-doctoral position in Pear Genomics and Biotechnology

by Dhingra, Amit

Post-doctoral position in Pear Genomics and Biotechnology A post-doctoral position is available immediately to study fruit ripening phenomenon in Pear utilizing genomics and biotechnology approaches. The project will focus on understanding the cold-temperature based ripening in certain Pear varieties using transcriptomics. Training in the areas of genomics, genetics and next-generation sequencing technologies and an interest in computational biology and breeding will be preferred. Applicants should have a Ph.D. in plant biology, molecular biology, biotechnology or horticulture. We are looking for a highly enthusiastic, self-motivated and a creative individual who is a critical thinker capable of independent thought and research and is highly desirous of utilizing this opportunity to advance their career. There are additional opportunities to contribute to the ongoing apple genome project in the laboratory. Excellent oral and written communication skills and the ability to work well in a collaborative research environment are essential. The successful candidate is expected to participate in outreach activities, training of graduate and undergraduate students and interact with fruit industry members. The initial appointment will be for one year and reappointment will depend on successful performance and availability of funding. Salary will be commensurate with experience and qualifications. Additional information on horticultural genomics and biotechnology program can be found at www.genomics.wsu.edu <http://www.genomics.wsu.edu/> . Please email your application along with detailed curriculum vitae to Dr. Amit Dhingra (Email: adhingra(a)wsu.edu). Also arrange for three letters of reference to be emailed directly to Dr. Dhingra. WSU employs only U.S. citizens and lawfully authorized non-U.S. citizens. All new employees must show employment eligibility verification as required by the U.S. Citizenship and Immigration Services. AA\EEO\ADA

17 years, 4 months

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Associate in Research Position in Horticultural Genomics and Biotechnology lab at WSU

by Dhingra, Amit

Associate in Research Position in Horticultural Genomics and Biotechnology lab at WSU A position for an Associate in Research position is available immediately in the Horticultural Genomics and Biotechnology laboratory at Washington State University. The incumbent will be self-motivated, proactive and a creative individual who can synthesize basic and applied approaches in plant biology research. Our program is sequencing the apple genome and uses high-throughput next-generation genomics platforms to resolve biological questions in horticultural crops grouped in Rosaceae and in grapes. The successful candidate will assist the PI in managing the laboratory, and perform research in various areas related to genomics, genetics, transcriptomics, computational biology and biotechnology. The person will be expected to participate in the laboratory's outreach activities. Excellent organizational and communication skills are required. In addition, computer skills for biological data analysis will be considered favorable. Familiarity with next-generation sequencing technologies will be advantageous. The person is expected to work with an interdisciplinary team and demonstrated ability to interact and work collaboratively with others will be considered favorably. The selected candidate is expected to design and conduct experiments independently, and to help in graduate, undergraduate student training. A MS in plant biology field is required. A Ph.D. in Plant Sciences or related discipline is preferred. A candidate with BS may be considered only if they have over 7 years of experience in a similar position. Good publication record is an advantage. Salary will be commensurate with experience. Additional information on horticultural genomics and biotechnology program can be found at www.genomics.wsu.edu <http://www.genomics.wsu.edu/> . Please email your application along with detailed curriculum vitae to Dr. Amit Dhingra (Email: adhingra(a)wsu.edu). Also arrange for three letters of reference to be emailed directly to Dr. Dhingra. WSU employs only U.S. citizens and lawfully authorized non-U.S. citizens. All new employees must show employment eligibility verification as required by the U.S. Citizenship and Immigration Services. AA\EEO\ADA

17 years, 4 months

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2009 Plant and Animal Genome Fruit and Nut Workshop - message from organizer Dr Nahla Bassil

by Main, Doreen

Dear Fruit and Nut Researchers, As organizer to the Fruit and Nut Workshop at the Plant and Animal Genome (PAG) XVII meeting, I am inviting you to e-mail me a title and a description for an oral talk that you would like to present at this workshop on Saturday, January 10th, 2009. I would like to ensure that new research information about the widest possible number of fruits and nuts are presented at this workshop and not status reports that can be presented as posters. Please e-mail me a possible title and a short paragraph describing your presentation by Wednesday, September 24th. Make sure to include: Fruit and Nut Workshop in the subject line. I will e-mail invitations on Friday, September 26th. The deadline for the abstracts is one week later, on Friday, October 3rd. Feel free to e-mail this request to anyone you would think would be interested. Your reply will be instrumental to the success of this workshop. Best regards, Nahla Bassil Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 bassiln(a)hort.oregonstate.edu nahla.bassil(a)ars.usda.gov Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

17 years, 5 months

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RosBREED

by Amy Iezzoni

Dear Colleagues, A few months ago, the US Rosaceae Genetics, Genomics and Breeding Executive Committee, under the leadership of Gennario Fazio, began discussing community initiatives. RosBREED: Enablling marker assisted breeding in Rosaceae, arose from these discussions. As a result of a conference call last week, a small committee was put together to further develop our vision and goals for this community project targeting submission to the fortcoming US Specialty Crop Research Initiative. I agreed to lead the effort at this point and I have tentatively agreed to PI the proposal, depending on the due date. I want to thank the committee, especially Cameron Peace and Jim Olmstead who had a late night last night, for preparing an excellent outline for your review. Our goal was to ground the outline solidly with a vision, mission and justification, yet also provide sufficient detail on the objectives and approach so that you can provide critique. We invite your comments and changes to the attached outline. Please use track changes for your edits etc. Upon reading the outline, you'll notice that under "Strategies to achieve objective 1", our goal is to test the robustness of marker trait associations over a wide range of germplasm (beyond the populations in which they were first discovered). To achieve this objective, I would like to ask for your help in compiling a list of available marker - trait associations. We will use this list as an in-house document from which we can select marker - trait associations for the proposed pipeline. Thank you in advance for your help. Both the outline and table are attached. I began adding to the table to get it started. Unfortunately we are working on a very tight deadline and so we would appreciate your comments, suggestions, and Table additions by next Wed if possible. We look forward to hearing from you and collaborating in any way possible. Best regards, Amy Dr. Amy Iezzoni Professor Department of Horticulture Michigan State University East Lansing, MI 48824 telephone: (517) 355-5191 ext. 391 fax: (517) 353-0890

17 years, 7 months

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Warning GDR will be unavailable from 5.30 to 10 PM PST on Monday May 19th

by Main, Doreen

Due to power configuration changes in the IT room housing our servers, GDR will be offline from 5.30 to 10 PM PST on Monday May 19th. I apologize for any inconvenience this may cause. Cheers Dorrie --------------------------------------------------------------------- Dorrie Main, PhD Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 ---------------------------------------------------------------------

17 years, 9 months

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Plant Ontology Database #0408 Release

by Chih-Wei Tung

Plant Ontology (PO) Consortium is happy to announce the release #0408 of the PO database! http://www.plantontology.org. For detailed release notes, please visit http://www.plantontology.org/docs/release_notes/index.html * Ontology - 1128 PO terms [19 NEW] - 58117 annotations [18572 NEW] * Ontology and annotation browser (http://www.plantontology.org/amigo/ go.cgi) - NEW: Added ~16000 annotations on genes and mutant phenotype germplasm from tomato, tobacco, potato, eggplant, pepper and Hyoscyamus. These annotations are contributed by Solanaceae Genomics Network (SGN; http://sgn.cornell.edu/) - Updated and added new annotations contributed by TAIR (for Arabidopsis) and Gramene (for rice) databases. * Publication - The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Avraham et al. Nucleic Acids Research 2008 36:D449-D454; http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 * Ontology requests - We encourage researchers to submit ontology requests at: http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 * Collaborators - We welcome our new collaborators: Dennis Stevenson: NY Botanical Graden Maria A. Gandolfo: Bailey Hortorium, Cornell University Bioversity International: http://www.bioversityinternational.org Generation Challenge Programme (GCP): http://www.generationcp.org The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po-dev at plantontology.org The project is funded by National Science Foundation, USA, (Grant No. DBI-0703908)

17 years, 10 months

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RosEXEC 2008 election RESULTS

by Peace, Cameron

Dear Rosaceae GGB community, Congratulations to EIGHT new RosEXEC members joining in 2008: U.S. RosEXEC members Nahla Bassil (USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR) Chris Dardick (USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV) Amit Dhingra (Washington State University, Pullman, WA) Jim Luby (University of Minnesota, St. Paul, MN) Gayle Volk (USDA-ARS, National Center for Genetic Resources Preservation, Fort Collins, CO) These five people will serve three-year terms. RosEXEC International Liaisons Jasper Rees (University of the Western Cape, South Africa) Dan Sargent (East Malling Research, United Kingdom) Eric van de Weg (Plant Research International, Netherlands) Note that although only two slots were offered for International Liaison,election results were so close for the three candidates above that we invite all three to join RosEXEC, to serve two-year terms. With the addition of these new members, we anticipate that the current momentum in U.S.-wide and international coordination and synergy will be maintained and ramped up even further. We appreciate the enthusiastic efforts over the last three years of our 2008 outgoing members, and look forward to their continued involvement in our community. New initiatives such as the RosCAP proposal submitted in February 2008 demonstrate the high level of cooperation we are experiencing in this community, resulting from strategic efforts led by RosEXEC over the last several years. This has been and will be possible only with interest and efforts from all of you. Vote counts were very close, and it is encouraging to realise that we have so many good people willing to devote their time to the objectives of RosEXEC. You don't have to be a member of RosEXEC to make a valuable contribution to furthering the ideals of our community. Within RosEXEC, the Secretary for 2008 will be elected in the next week or so. Congratulations again to our new RosEXEC members for 2008. RosEXEC Membership Committee

17 years, 10 months

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RosEXEC elections - last chance to vote!

by Peace, Cameron

Dear Rosaceae GGB community, Only one day left for voting for five new U.S. RosEXEC members and two RosEXEC international liaisons. Polls close 5:00 pm PST (Friday April 4). Anyone that is U.S.-based and interested in genomics, genetics, and/or breeding of rosaceous crops is eligible to vote. Conceivably, this includes about 200 million people, but it at least includes industry personnel, educators, extension agents, administrators, students, and avid consumers, in addition to the 25 mostly genomicists, geneticists, and breeders who have already voted. So if you have not yet expressed your preferences, please hop on to www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2008_vote_form.cgi <https://connect.wsu.edu/exchweb/bin/redir.asp?URL=http://www.bioinfo.wsu.ed…> and vote! Please also direct your Rosaceae GGB colleagues to this site (and encourage them to also sign up for the GDR mailing list if they aren't already on it). Across the country, we all have a voice in future directions of the U.S. Rosaceae genomics, genetics, and breeding initiative. Currently, only one vote separates U.S. candidates running 3rd, 4th, 5th and 6th. Only one vote also separates 1st, 2nd, and 3rd positions for international liaison candidates. Each new vote WILL COUNT! The RosEXEC Membership Committee

17 years, 10 months

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International Working Group on Comparative Mapping

by Dan Sargent (EMR)

Dear Rosaceous Genomics Community members. During the recent Rosaceous Genomics Conference in Chile, it was decided that there should be a coordinated community effort towards comparative mapping, and that we should set up an international working group to attempt to meet these aims. I volunteered to act as interim chair of this working group whilst it is established and therefore I am currently drawing up a list of people from the community with an interest in comparative mapping and transferable markers with whom I will communicate over the coming weeks. I have already identified a number of people within the community who are working on topics related to comparative mapping, but I want to be as inclusive as possible, so if you have a wish to be a part of any correspondence relating to this working group and/or want to be involved in this community effort, then please could you email me at dan.sargent(a)emr.ac.uk? Once I have a list of interested people, I will be contacting you further. Ideally I would like to have responses from interested parties by the end of next week (11th April 2008) so that I can get some kind of GDR mailing list sorted out etc. I will look forward to hearing from you all in the near future, All the best Dan Sargent Dr Daniel James Sargent East Malling Research New Road East Malling Kent ME19 6BJ, UK dan.sargent(a)emr.ac.uk Telephone: +44 (0) 1732 523 747 Fax: +44 (0) 1732 849 067 East Malling Research registered office: New Road, East Malling, Kent ME19 6BJ. Tel. 01732-843833. Registered in England No. 5019373. Charity registration No.1102243. The information in this E-Mail and any attachments is confidential, may be legally privileged and is intended to be for the use of the intended recipient/s. If you are not the recipient named above please be aware that any disclosure, copying, distribution or use of the contents of this information is prohibited and may not represent the views of EMR. Activity and use of the East Malling Research E-mail system and any communications using it are monitored to secure its effective operation and for other lawful business purposes.

17 years, 10 months

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RosEXEC ELECTIONS 2008

by Peace, Cameron

RosEXEC ELECTIONS 2008 The US Rosaceae Genomics, Genetics, and Breeding Executive Committee (RosEXEC) will be electing five new members to replace outgoing members. RosEXEC serves as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics, and breeding (GGB) community. We have four objectives: 1. Define research priorities based on input from the industry and the research community 2. Foster scientific interaction and dynamic research teams 3. Promote research priorities 4. Coordinate educational efforts from the research community to the industry and the public RosEXEC meets in person at annual Plant and Animal Genome conferences and holds quarterly teleconferences. In 2008, Kevin Folta is the outgoing Chair and Gennaro Fazio is the incoming Chair. More information on RosEXEC can be found on the GDR at www.bioinfo.wsu.edu/gdr/community/rosexec/, including a list of all 2007 members (www.bioinfo.wsu.edu/gdr/community/rosexec/membership/index.shtml). The election process is only open to U.S.-based Rosaceae GGB community members, regardless of citizenship. Up to five votes can be cast per person. Please strive to represent the diversity of our community by electing candidates from various crop interests, institutional affiliations, and geographical locations. Elections will be held electronically via the GDR at www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2008_vote_form.cg i. The US RosEXEC Membership Committee has suggested some candidates on the voting form posted on the GDR, and we urge interested community members to nominate other qualified candidates: this can be done via the voting page, or by directly contacting Cameron Peace (cpeace(a)wsu.edu). Outgoing RosEXEC members (Herb Aldwinckle, Amy Iezzoni, Kim Lewers, and Jim McFerson) are not eligible for re-election until 2009. New US RosEXEC members will be selected by vote totals and will serve three-year terms. Please note that you can also nominate and vote on up to two members as International Liaisons for the U.S. RosEXEC. Current members are Sue Gardiner and Herman Silva, with Pere Arus revolving off. We will add two new international liaisons in 2008, who will serve two-year terms. If you have any problems using the voting page, please email Dorrie Main (dorrie(a)wsu.edu). The deadline for voting is in one week: Friday 4 Apr 2008, 5pm PST. Cameron Peace, on behalf of the RosEXEC Membership Committee

17 years, 10 months

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Biotechfruit2008

by V.Hanke

ISHS Commission Biotechnology and Molecular Biology BIOTECHFRUIT2008 First International Symposium on Biotechnology of Fruit Species ABSTRACT SUBMISSION DATE IS EXTENDED TO MARCH 31, 2008 Dear Colleagues, We cordially invite you to the First International Symposium on Biotechnology of Fruit Species. The meeting will be held in Dresden, Germany from September 1 - 5, 2008. This Symposium builds on the previous symposia of tropical and subtropical species and follows the very successful Symposium in Daytona, Florida in 2005, which covered biotechnology and transformation of tropical and temperate species. The Symposium in Dresden will explore the progress being made in temperate, tropical and subtropical fruit species. The purpose is to provide a forum for scientists to share their results and experiences in the application of different biotechnology tools for genetic improvement of fruit crops. This meeting will foster interactions amongst research groups from developing and developed countries from all over the world. For further information including details for submission of abstracts, please visit the symposium website http://www.biotechfruit2008.bafz.de/ Or email the Symposium Secretariat on biotechfruit2008(a)bafz.de < <mailto:biotechfruit2008@bafz.de> mailto:biotechfruit2008@bafz.de> We look forward to meeting you in Dresden in September 2008. Warm regards, Viola Hanke On behalf of the Organising Committee Dr. habil. Magda-Viola Hanke Julius Kuehn-Institute (JKI) Federal Research Centre for Cultivated Plants Pillnitzer Platz 3a 01326 Dresden, Germany e-mail viola.hanke(a)jki.bund.de Tel. ++49-351-2616214 Fax ++49-351-2616213 www.jki.bund.de

17 years, 10 months

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RGC4 bin-set development mini-workshop

by Peace, Cameron

Dear Rosaceae Genomics community, Especially for those genetic mappers among you who will be attending RGC4 in a few days, you are invited to a 2-hour mini-workhop on how to create your own bin-set, hosted by Cameron Peace and Werner Howad. We will also provide an overview and update of RosPOP (The Rosaceae Consortium of Mapping Populations; www. bioinfo.wsu.edu/gdr/community/international/rospop.shtml). When: Sunday March 16th 13:30- 15:30 (i.e. during Registration) Where: Araucania Salon An agenda for this mini-workshop follows. Learn how to develop an informative subset of your mapping population, or share your own experiences. This will be an informal meeting based on the community approach of RosPOP. 13:30-13:45 RosPOP overview 13:45-13:50 Update on RosPOP setup on the GDR 13:50-14:00 General discussion on RosPOP 14:00-14:20 Bin-mapping overview 14:20-14:30 General discussion on bin-mappping 14:30-15:10 How to create a bin-set (whether you have a saturated or a less-than-perfect map) 15:10-15:30 General discussion on how to create a bin-set We look forward to seeing you in Pucon! Cameron Peace & Werner Howad

17 years, 11 months

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Extension for submission of abstracts to March 31.

by Gennaro Fazio

Dear Colleagues, We are planning to have a session on genomics, genetics of rootstocks and rootstock/scion interactions and another session on rootstock breeding in August 2008 as part of the ISHS Orchard systems, rootstocks and environmental physiology symposium. I am hoping that you will submit an abstract and participate in that session and other sessions of the symposium. We have extended the deadline to submit abstracts until March 31, 2008 for the upcoming ISHS Orchard systems, rootstocks and environmental physiology symposium which will be held Aug. 4-8, 2008 at Geneva, New York, USA. We invite you to submit an abstract and look forward to seeing you in Geneva. For complete information on the symposium and to submit abstracts please visit the symposium website http://www.nysaes.cornell.edu/hort/ishs/ All the best, Gennaro Fazio, PhD Apple Rootstock Breeder and Geneticist Plant Genetic Resources Unit USDA ARS Cornell University - 630 W. North St. Geneva, NY 14456 (315) 787-2480 Office (315) 787-2216 Fax

17 years, 11 months

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RGC4 NEWS & UPDATE

by Ariel Orellana López

******************************************************************************************************************************************************************* 4th Rosaceae Genomics Conference UPDATE AND NEWS IMPORTANT: On February 16 the registration fees will increase in $100 US dollars, so we really encourage you to register early. If you haven't registered or sent your Abstract we urge you to do so ASAP! We are in the final stages of organizing the abstracts and the scientific committee will be reviewing them this week. We would like to thank everyone who has sent us their abstracts in word or pdf format. If you haven't sent it to us yet, please send it ASAP. We would also like to let you know that there are a limited number of fellowships for graduate students. This fellowship will include shared housing in an apartment complex as well as the hotel's meal program. Those who are interested in applying for this fellowship should fill out the form that appears on the rgc4 website as well as present proof that they are enrolled in a graduate program. PLEASE NOTE: THIS FELLOWSHIP DOES NOT INCLUDE REGISTRATION. THE STUDENT MUST STILL CANCEL THE STUDENT REGISTRATION FEE. The deadline to present Student Fellowship Applications is February 22nd. APPLICATIONS WILL NOT BE ACCEPTED AFTER THIS DATE!! The abstracts that we have received are very interesting and from many countries throughout the world, suggesting that this conference will be a great opportunity to for us to discuss the international advances in Rosaceae genomics as well as get to know each other more socially. We look forward to seeing you "at the end of the world". Saludos, Organizing Committee Lee Meisel Eliseo Campos Ariel Orellana Chair of the Scientific Committee Herman Silva

18 years

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News and Update RGC4

by Sook Jung

4th Rosaceae Genomics Conference UPDATE AND NEWS We have been getting a great number of contributions for RGC4!!!By looking at the titles submitted, it looks like it will be a great time for Rosaceae Genomics. You can not miss this great event!! As January 14 we have received 90 abstracts. If you missed the abstract deadline, please notice that you still have a few days to send your abstract to be considered for an oral presentation. IMPORTANT: In order to have the proper printing of the abstracts we ask all the submitters to send their abstracts in a word or pdf document. Please send the document via email to rgc4(a)unab.cl Regarding registration, we had a few problems with the payment online however, now is running normally. Please, if you detect any trouble with the system, let us know to fix it as soon as possible Shortly we will add contact information regarding activities in the Pucon area before and after the meeting as well as special arrangements that attendants may need in order to stay at the Gran Hotel Pucon (www.granhotelpucon.cl) We look forward to seeing all of you at this meeting so that we can discuss the scientific advances as well as enjoy what Chile has to offer. Please join us at the 4th International Rosaceae Genomics Conference in Pucon, Chile . Decisions on Oral Presentation and Poster Abstract. February 10, 2008 Early bird registration closes February 15, 2008 We look forward to seeing you in Chile !!! Saludos, Organizing Committee Lee Meisel Eliseo Campos Ariel Orellana Chair of the Scientific Committee Herman Silva

18 years, 1 month

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RosEXEC phone access number for the Meeting on January 13.

by gf35＠cornell.edu

As many of you already know the Rosaceae Executive Committee will hold a meeting in San Diego on January 13 in the Towne Room starting at 8:00 AM Pacific Time. I have set up a teleconferencing meeting and will probably have my crll phone on speaker phone. Below is the Toll Free Number to access the conferencing service and the Passcode. Email me Gennaro.fazio(a)ars.usda.gov if you need more international access numbers. Participant Passcode: 2402523 USA 1-517-466-2232 866-692-3582 ITALY 39-02-3600-6016 800-986-993 UNITED KINGDOM BIRMINGHAM: 44-121-210-9039 0808-238-6019 UNITED KINGDOM GLASGOW: 44-141-202-3239 0808-238-6019 UNITED KINGDOM LEEDS: 44-113-301-2139 0808-238-6019 UNITED KINGDOM LONDON: 44-20-3043-2499 0808-238-6019 UNITED KINGDOM MANCHESTER: 44-161-601-1439 0808-238-6019 All the best, Gennaro Gennaro Fazio, PhD Apple Rootstock Breeder and Geneticist Plant Genetic Resources Unit USDA ARS Cornell University - 630 W. North St. Geneva, NY 14456 (315) 787-2480 Office (315) 787-2216 Fax

18 years, 1 month

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RosEXEC phone access number for the Meeting on January 13.

by Fazio, Gennaro

As many of you already know the Rosaceae Executive Committee will hold a meeting in San Diego on January 13 in the Towne Room starting at 8:00 AM Pacific Time. I have set up a teleconferencing meeting and will probably have my crll phone on speaker phone. Below is the Toll Free Number to access the conferencing service and the Passcode. Email me Gennaro.fazio(a)ars.usda.gov if you need more international access numbers. Participant Passcode: 2402523 USA 1-517-466-2232 866-692-3582 ITALY 39-02-3600-6016 800-986-993 UNITED KINGDOM BIRMINGHAM: 44-121-210-9039 0808-238-6019 UNITED KINGDOM GLASGOW: 44-141-202-3239 0808-238-6019 UNITED KINGDOM LEEDS: 44-113-301-2139 0808-238-6019 UNITED KINGDOM LONDON: 44-20-3043-2499 0808-238-6019 UNITED KINGDOM MANCHESTER: 44-161-601-1439 0808-238-6019 All the best, Gennaro Gennaro Fazio, PhD Apple Rootstock Breeder and Geneticist Plant Genetic Resources Unit USDA ARS Cornell University - 630 W. North St. Geneva, NY 14456 (315) 787-2480 Office (315) 787-2216 Fax

18 years, 1 month

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GDR computer demo at PAG-XVI

by Sook Jung

Dear colleagues, We would like to let you know that GDR will present a computer demo this Sunday afternoon at PAG-XVI in San Diego, CA. Title: GDR (Genome Database for Rosaceae): Integrated Web-Database for Rosaceae Genomics and Genetics Data Time: January 13 (Sun) 4:15 pm-4:35 pm (Computer Demo Part I: 3:35 pm-5:45 pm) Place: California Room, Town&Country Convention Center, San Diego, CA Poster number: P928 We look forward to meeting you there! Sook Jung Washington State University

18 years, 1 month

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Plant Ontology Computer Demo in PAGXV, 13 January 2008

by Chih-Wei Tung

Dear colleagues, We are pleased to inform you that Plant Ontology Consortium will host a 20-minutes computer demo in Plant & Animal Genome XV (PAGXV), San Diego, CA. http://www.intl-pag.org/16/16-demos.html Title: The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations Time: January 13, 5:35pm-5:55pm Place: California Room, Town&Country Convention Center, San Diego, CA Poster number: P931 We look forward to meeting you! If you are not attending the conference, please feel free to browse/download our poster at http:// ascus.plbr.cornell.edu/~gramene/poc/PAG2008 Thank you, Chih-Wei Tung Plant Ontology Consortium Cornell University Ithaca, NY 14850

18 years, 1 month

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Rosaceae Executive Committee Elections.

by Sook Jung

Dear Rosaceae Community, On behalf of the US Rosaceae Executive Committee I would like to extend an invitation to industry representatives and scientists to participate in this committee whose mission is to serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community (more information about the mission can be found on GDR http://www.bioinfo.wsu.edu/gdr/community/rosexec/ . This year we need to fill five slots on the committee and elect a new secretary. I have been impressed by the work of this committee and urge you to take this opportunity to participate in the coordination process during this crucial time for Rosaceae Genomics. If you are interested in participating please contact the current membership chairs Jim McFerson McFerson(a)treefruitresearch.com or Herb Aldwinckle hsa1(a)cornell.edu or Gennaro.Fazio(a)ars.usda.gov or Cameron Peace cpeace(a)wsu.edu and indicate your availability. We hope to have a ballot by our next meeting at PAG (Sunday Jan. 13 at 8 AM in the Towne Room) and hold elections shortly thereafter. All the best, Gennaro Gennaro Fazio, PhD Apple Rootstock Breeder and Geneticist Plant Genetic Resources Unit USDA ARS Cornell University - 630 W. North St. Geneva, NY 14456 (315) 787-2480 Office (315) 787-2216 Fax

18 years, 1 month

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Post-doctoral position

by Dardick, Chris

I would like to send out an announcement for the following post-doctoral position. If possible, I would also like to post it on the GDR community news. thanks, Chris Research Molecular Biologist (Virologist) Appalachian Fruit Research Station Kearneysville, WV Salary Range: $55,706 to $72,421 USD Per Year These are the 2007 salary rates, salary increase proposed for January 2008 The ARS, North Atlantic Area is seeking highly qualified candidates for a temporary full-time scientific position. The position is located at the Appalachian Fruit Research Station in Kearneysville, West Virginia which is situated approximately 65 miles North West of Washington D.C. The Unit's overall mission is the genetic improvement of important agronomic traits in tree fruits (peaches, plums, and pears) such as architecture, fruit quality, and disease resistance. The incumbent will be responsible for identifying and characterizing host genes and host responses that mediate susceptibility to plum pox potyvirus. Research will focus on engineering plum pox resistance through the characterization and transgenic manipulation of host genes in plum as well as more basic functional genomic studies on potyvirus-host interactions using tree fruits and herbaceous model systems. Infection studies using plum pox virus, a quarantined agent, will be performed in the BSL-2/3 biocontainment facilities located in nearby Fort Detrick, Maryland. The scientist will be responsible for disseminating research results at scientific meetings and in peer-reviewed scientific publications. Information on salary and application procedures for this Postdoctoral Position is available at: http://www.afm.ars.usda.gov/divisions/hrd/hrdhomepage/vacancy/pd962.html <http://www.afm.ars.usda.gov/divisions/hrd/hrdhomepage/vacancy/pd962.htm l> RA-08-007H USDA is an equal opportunity employer. Women and minorities are encouraged to apply. For more information please contact: Chris Dardick USDA, ARS Appalachian Fruit Research Station 2217 Wiltshire Road Kearneysville, WV 25430 phone: 304-725-3451 ext. 387 fax: 304-728-2340 chris.dardick(a)ars.usda.gov

18 years, 2 months

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Pome Fruit Breeder/Geneticist Vacancy at Washington State University

by Main, Doreen

NOTICE OF VACANCY Pome Fruit Breeder/Geneticist (Apples) Washington State University Search #4873 WORKING TITLE: Pome Fruit Breeder/Geneticist 15% Academic Programs /85% Agricultural Research Center RANK: Assistant Professor or Associate Professor, 12-month, tenure track LOCATION: Washington State University (WSU) Tree Fruit Research and Extension Center (TFREC), Wenatchee, Washington SALARY: Competitive and commensurate with training and experience. EFFECTIVE: July 1, 2008 GENERAL DESCRIPTION: Washington State is the leading producer of apples, pears, and sweet cherries in the U.S., with more than 200,000 (180,000 apple) acres of tree fruits statewide valued at more than $6 billion annually. The TFREC in Wenatchee is central to this large production region. The Yakima Valley and Columbia Basin, easily accessible from Wenatchee, remain as some of the most agriculturally-diverse regions of the U.S. These regions are also major producers of tree fruits in addition to many other high-value horticultural crops. The long, warm summer days, cool nights, low precipitation, and volcanic soils make the area ideal for irrigated fruit production. Washington State University is the state's land grant university with teaching, research, and extension missions. The Washington State University Department of Horticulture and Landscape Architecture is located on the main campus in Pullman, with research locations and faculty in seven other locations throughout Washington State. As a result of recent strategic hires, Rosaceous genetics, genomics and plant breeding have emerged as a preeminent area within the Department of Horticulture and Landscape Architecture and within the College. The Orville A. Vogel Plant Biosciences Building on the Pullman Campus, the first of five under construction or planned in the Biotechnology Complex opened in 2005, features new state-of-the-art teaching and research facilities in support of an expanded university-wide effort in this area. A recently published analysis ranks Plant Science research productivity at Washington State University in the top echelon. This position is located at the Tree Fruit Research and Extension Center (TFREC) in Wenatchee, located in one of the principal production areas in Washington State. The TFREC is one of several research centers of the College of Agricultural, Human, and Natural Resource Sciences. Comprehensive research projects are conducted by Washington State University and United States Department of Agriculture (USDA) collaborating scientists in all phases of orchard culture, pest control, fruit harvesting and handling, fruit maturity, storage, grading and packaging. These programs also include basic science aspects of plant physiology, entomology, plant pathology, soil science, horticulture, economics and biochemistry. Research programs at the TFREC emphasize primarily apples, pears and sweet cherries although some research is conducted on apricots, peaches and plums. Research is also conducted in orchards of cooperating growers throughout the major fruit production areas of Washington. Production and postharvest research by USDA scientists is also conducted using grower orchards and in cooperation with fruit packinghouses. The core of the facilities is the main center campus located in Wenatchee which includes office, laboratory, and greenhouse space for WSU and USDA scientists. A newly dedicated state-of-the-art research orchard in Wenatchee provides field research facilities for these same scientists plus those from the main Pullman campus and other research centers around the state. The Washington Tree Fruit Research Commission uses grower assessments on fruit produced in the state to provide funds to conduct a substantial research effort in partnership with WSU on every aspect of tree fruit production, from germplasm and rootstock development to improved post-harvest practices as well as sensory eating quality. Approximately $3 million per year is invested in tree fruit research grants, with funding based on the proportion of dollars collected for each tree fruit commodity. RESPONSIBILITIES: The incumbent will lead the WSU Department of Horticulture and Landscape Architecture pome fruit breeding and genetics research and extension program, with emphasis on the use of modern genetic and genomic research tools to assist in the creation of new apple varieties specifically suited to production in the Pacific Northwest. The program complements other Tree Fruit Research and Extension Center (TFREC) initiatives, such as tree fruit physiology, tree fruit virology, disease forecasting, post-harvest biology/technology, and integrated pest management. The research program will focus on the use of modern genetic and genomic research tools to create new apple varieties, continuation and enhancement of the established apple breeding program, and maintenance and evaluation of the existing apple germplasm collection at Wenatchee. The incumbent's program will complement other breeding, genetics, and genomics programs in the Department of Horticulture and Landscape Architecture that focus on stone fruit, raspberry, and strawberry. Opportunities may also emerge for future work on pears. The successful candidate will emphasize collaborative programs with state, federal, and private research and extension personnel to strengthen an interdisciplinary horticultural breeding, genetics, and genomics team. The successful candidate will actively pursue extramural research funding, contribute scholarly literature, and enhance the national and international scope of the WSU apple breeding program. The successful applicant will be expected to conduct an approved program of research consistent with the mission of the WSU Agricultural Research Center. The incumbent will be expected to work effectively with extension specialists and area agents, private crop consultants, and with the grower community and stakeholders. The incumbent will participate in regional meetings, promote apple varieties, and write for popular/grower press in addition to publishing in scientific journals. Teaching responsibilities will include classroom instruction in fruit breeding and genetics, and the mentoring and supervision of graduate and undergraduate students. QUALIFICATIONS: Required: 1) Ph.D. in horticulture or a related plant science discipline at the time of hire. 2) Evidence of scholarly accomplishments in fruit breeding, genetics, and genomics. 3) Demonstrated ability to communicate effectively with technical and non-technical audiences in oral, written, and electronic forms. Highly Desired: 1) Excellent abilities in research, teaching, and team building. 2) Evidence of potential for acquiring extramural grant support. 3) Knowledge of field research in tree fruit breeding. 4) Knowledge of state-of- the-art genetic and genomic techniques. LOCATION: The Greater Wenatchee Area has a population of 37,300 and straddles the Columbia River in the center of Washington. In addition to excellent primary and secondary schools, Washington State University offers upper-division and graduate-level courses and programs through distance-learning opportunities located on the Wenatchee Valley College campus. Wenatchee is located on the eastern edge of the Cascade Range, thus providing abundant recreational opportunities. In addition to local attractions, year-round art and cultural events, and a thriving seasonal farmer's market, the City of Seattle and the greater Puget Sound Region lie 150 miles to the west. APPLICATION PROCESS: Screening of application materials will begin January 15, 2008. A letter addressing qualifications, a statement of professional vision and goals, a detailed resume with publication list, copies of official college/university transcripts, and three current, signed letters of reference (direct from the source) must be provided. Send this application packet to: Dr. John Fellman, Search Chair Department of Horticulture and Landscape Architecture Washington State University P.O. Box 646414 Pullman, WA 99164-6414 509-335-3454 (voice), 509-335-8690 (fax), fellman(a)wsu.edu For information on application status, contact Ms. Bev Brantner at 509-335-3943 or brantner(a)wsu.edu. WASHINGTON STATE UNIVERSITY IS AN EQUAL OPPORTUNITY/AFFIRMATIVE ACTION EDUCATOR AND EMPLOYER. Members of ethnic minorities, women, special disabled veterans, veterans of the Vietnam-era, recently separated veterans, and other protected veterans, persons of disability and/or persons age 40 and over are encouraged to apply. WSU employs only US citizens and lawfully authorized non-US citizens. All new employees must show employment eligibility verification as required by the U.S. Citizenship and Immigration Services. Washington State University is committed to providing access and reasonable accommodation in its services, programs, activities, education and employment for individuals with disabilities. To request disability accommodation in the application process, contact Human Resource Services: 509-335-4521(v), Washington State TDD Relay Service: Voice Callers: 1-800-833-6384; TDD Callers: 1-800-833-6388, 509.-335-1259(f), or hrs(a)wsu.edu <mailto:hrs@wsu.edu> Beverly Brantner, Program Coordinator Horticulture & Landscape Architecture Washington State University PO Box 646414 Pullman, WA 99164-6414 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Johnson Hall 149 Phone 509-335-3943 Fax 509-335-8690 brantner(a)wsu.edu <mailto:brantner@wsu.edu>

18 years, 2 months

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Title submission for RGC4

by Sook Jung

Dear Colleagues, I'm forwarding the message regarding the title submission for RGC4. The deadline is extended for a week and due on Nov. 7. Thanks, Sook Jung ---------- Forwarded message ---------- From: Ariel Orellana <aorellana(a)unab.cl> Date: Oct 31, 2007 2:57 PM Subject: Title submission for RGC4 To: sook(a)bioinfo.wsu.edu Cc: lmeisel(a)unab.cl Dear Sook: I would appreciate your help on sending the following message to the rosaceae community. Dear members of the rosaceae community: Just a reminder that the deadline for title submission of work to be presented at the RGC4 meeting is today, however, we will extend this deadline for 1 week. The other important deadline is the abstract submission by December 31. Please, check the web page www.rgc4.cl to submit your title. if you have any trouble uploading your title, please send a message with the information to rgc4(a)unab.cl Sincerely Ariel Orellana Lee Meisel

18 years, 3 months

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RosCAP Team proposals

by Dardick, Chris

Dear Colleagues, The RosCAP Team Guidance Committee would like to thank you for your efforts in organizing teams and preparing pre-proposals in such a short time frame. We received a total of 8 proposals (3 malus, 2 fragaria, 2 prunus, 1 Rosoideae) that span a wide range of crops, traits, and approaches. We do not view this as a competitive process and our goal is to include as many teams and as many aspirations as possible into the final RosCAP proposal. Our sincere hope is that all (or aspects of all) can be included. After an initial review, we will be contacting the team leaders for further discussions. Best Regards, RosCAP Team Guidance Committee (Chris Dardick, Amy Iezzoni, Schuyler Korban, Eric van de Weg) Chris Dardick USDA-ARS Appalachian Fruit Research Station Kearneysville, WV 25430 (304) 725-3451 ext. 387 chris.dardick(a)ars.usda.gov

18 years, 4 months

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FW: RosCAP website

by Dardick, Chris

________________________________ From: Bert Abbott [mailto:aalbert@CLEMSON.EDU] Sent: Wednesday, October 17, 2007 11:47 AM To: Dardick, Chris Subject: Re: RosCAP website Chris, here is a pdf. of the CAP portion of the NRI RFA. Please send it to all so that they can see the emphasis. Also note that the amount is 5 million for 4 years but that these are envisioned to be continuation type projects with continued funding. Bert

18 years, 4 months

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RosCAP proposal committees

by Dardick, Chris

Dear Rosaceae Community, Bert Abbott recently met with Debbie Sheely and Ed Kaleikau regarding a RosCAP proposal and received some very positive feedback: "When questioned about whether this was the right time for a CAP proposal from our community, I was given the distinct impression that we were in the right place at the right time. With the farm bill emphasis on specialty crops, Ed felt that this was indeed very timely." The deadline for the RosCAP letter of intent is closing fast (November 26th) and we need volunteers to quickly move the RosCAP forward. The RosCAP Proposal Guidance Committee has put together a list of committees and their tasks which must be accomplished ASAP. Activities include refinement of the education and extension components, schemes for marker development and marker-trait associations, as well as plans for web portal development and bioinformatics. For most of the committees we still need co-chairs in addition to volunteers willing to serve as committee members. If you previously volunteered at the Rosaceae Planning Meeting and your name is already listed, please confirm your willingness to participate. Your participation will be essential for a successful RosCAP proposal and would be greatly appreciated by all. Please contact Cameron Peace (cpeace(a)wsu.edu) or Chris Dardick ( chris.dardick(a)ars.usda.gov) if you would like to volunteer and indicate which committee(s) and whether or not you are willing to serve as a co-chair. Thank You, RosCAP Proposal Guidance Committee (Cameron Peace, Chris Dardick, Bert Abbott, Gennaro Fazio, Sue Gardiner, Amy Iezzoni, Schuyler Korban, Herman Silva, Eric van de Weg) Chris Dardick USDA-ARS Appalachian Fruit Research Station Kearneysville, WV 25430 (304) 725-3451 ext. 387 chris.dardick(a)ars.usda.gov

18 years, 4 months

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Call for RosCAP team proposals

by Main, Doreen

Dr. Amy Iezzoni Professor Department of Horticulture Michigan State University East Lansing, MI 48824 telephone: (517) 355-5191 ext. 391 fax: (517) 353-0890

18 years, 5 months

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Zaragoza

by riccardo.velasco＠iasma.it

18 years, 5 months

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Ros IGI meeting at EUCARPIA

by Main, Doreen

Hi everybody, I have had one reply from my earlier email to you - see below - so have had an easy job drawing up a tentative agenda for our RosIGI meeting in Zarogoza. There are exciting things going on, what with whole genome sequencing and a big project proposal for Rosaceae genomics applications in the US (RosCAP). I'm loooking forward to seeing those of you who can make it to Spain! Best wishes, Sue ________________________________ From: Sue Gardiner Sent: Monday, 3 September 2007 11:48 a.m. To: 'lewersk(a)ba.ars.usda.gov'; 'jasper(a)cil.biotech.uwc.ac.za'; 'Korban(a)uiuc.edu'; 'jwolmstead(a)wsu.edu'; 'riccardo.velasco(a)iasma.it'; 'angela.baldo(a)ars.usda.gov'; 'mvandyke(a)uwc.ac.za'; Emily Buck; Jean-Marc Celton; 'iezzoni(a)msu.edu'; 'foucher(a)angers.inra.fr'; 'mam262(a)cornell.edu'; 'eb31(a)cornell.edu'; 'slovinj(a)ba.ars.usda.gov'; 'aorellana(a)unab.cl'; 'd-byrne(a)tamu.edu'; 'pere.arus(a)irta.es'; 'toshiya(a)affrc.go.jp'; Sue Gardiner; 'tom.davis(a)unh.edu'; 'dorrie(a)wsu.edu'; 'tzhebe(a)clemson.edu'; 'ann.callahan(a)ars.usda.gov'; 'cpeace(a)wsu.edu'; 'chris.dardick(a)ars.usda.gov'; 'werner.howad(a)irta.es'; 'jill.bushakra(a)driscolls.com'; 'sjung(a)clemson.edu'; 'decroocq(a)bordeaux.inra.fr'; 'adhingra(a)wsu.edu'; 'sosinski(a)ncsu.edu'; 'RFolta(a)ufl.edu'; 'ebenezer(a)uckac.edu'; 'gvolk(a)lamar.colostate.edu'; 'cornb(a)ars.grin.gov'; 'deparfitt(a)ucdavis.edu'; 'FBLiss(a)dcn.org'; 'gvansickle(a)caltreefruit.com'; 'mcferson(a)treefruitresearch.com'; 'michael.wisniewski(a)ars.usda.gov'; 'jay.norelli(a)ars.usda.gov'; 'hsa1(a)cornell.edu'; 'csimon(a)ars-grin.gov'; 'zhu(a)tfrl.ars.usda.gov'; 'skb3(a)cornell.edu'; 'gennaro.fazio(a)ars.usda.gov' Cc: 'rsocias(a)aragon.es'; Richard Volz; Allan White; Vincent Bus; Roger Hellens; Andrew Granger Subject: Ros IGI meeting at EUCARPIA Hi all, - There will be a meeting of RosIGI (International Rosaceae Genomics Initiative) at the Zaragoza 12th EUCAPIA Symposium on Fruit Breeding and Genetics on Mon 17th September. I have been advised by the programme organizers that the advertized meetings that afternoon will take place in sequence rather than simultaneously; this is a great relief as most of us need to attend more than one meeting. - I attach the minutes of our previous meeting at PAG XV in January. I am sorry I did not distribute these earlier, they got buried under other events. I am addressing this email initially to you who attended, and will distribute the message more widely through GDR. My apologies to those who get the message twice - if you know folk who would be interested and don't appear to be on either lists please forward the message to them. We need to make up an agenda of the most urgent items - we are unlikely to have more than an hour for our meeting! Suggestions so far include: White Paper Brief updates on sequencing programmes News on RGC4 Please send items to me by the end of this week, so I can send the agenda out before I leave NZ for Spain. See you in Spain! Sue PS It is raining most days here and I can't wait to get to Spain, it is my very first visit there. ___________________________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. ___________________________________________________________________

18 years, 5 months

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Plant Ontology Database Release-September 2007

by Chih-Wei Tung

Plant Ontology Consortium is happy to announce the release #0907 of PO database! http://www.plantontology.org * Ontology update - 1109 PO terms - 32104 annotations visit http://www.plantontology.org/docs/release_notes/index.html for more details * New version of PO browser (http://www.plantontology.org/amigo/go.cgi) - New interface - New users guide - New tutorials - New feature: added "GO" (Gene Ontology) associations link to Arabidopsis genes * POC Website updates (http://www.plantontology.org/) - added "Request PO terms" feature on navigation menu - added "POC Outreach Activities" link in "Documentation" page - Updated "Mail Archives" - Updated "PO website usage statistics" - Updated "Tutorials" * POC and plant community - Welcome experts from Medicago, Populus, Rosaceae, Solanaceae, Vitis fields to join plant ontology development Please email to po-dev(a)plantontology.org or subscribe po-dev mailing list - Phenote (a phenotype annotation tool using ontologies http:// www.phenote.org/) has added "plant" configuration, plus PO and other plant related ontologies for curation. Contact Nicole Washington ( NLWashington(a)lbl.gov ) for more information about downloading and using Phenote tool - Meet POC members in international conferences @ 8th Agricultural Ontology Service (AOS) workshop, Rome, Italy Sep 21-22 @ 5th International Symposium of Rice Functional Genomics, Tsukuba, Japan Oct 15-17 @ 2nd International Biocuration meeting, San Jose, CA Oct 25-28 The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po-dev(a)plantontology.org submit requests at: http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555

18 years, 5 months

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Standardized Phenotyping in Rosaceae

by Peace, Cameron

Standardized Phenotyping in Rosaceae A new initiative in the international Rosaceae genomics, genetics, and breeding community! With a shared ancestral genome, the details of which are beginning to come to light from structural and comparative genomics research, the possibility exists to discover common gene networks underlying traits of interest to crops of the Rosaceae family. Techniques in genomics and bioinformatics are rapidly expanding for such comparative efforts, and the bottleneck is now the availability of readily comparable phenotypic data. Recent meetings on this topic in the US held by Gayle Volk, involving germplasm curators, breeders, and researchers, have begun to identify the challenges in obtaining phenotypic data that can be meaningfully transferred across Rosaceae germplasm sets. Standardized phenotyping can be as "simple" as aligning data collection methods for a crop between two research locations, or between a breeding program and a genomics research study. It is more difficult to obtain phenotypic data for two different crops, particularly across subfamilies, that have the likelihood of being under common genetic control. Achieving this goal, however, holds the promise of strengthening Rosaceae-wide ties between breeding programs, germplasm collections, and genetics and genomics research. The Standardized Phenotyping webpage is being created on the GDR (thanks Dorrie!). At first, the site will contain lots of background material and minutes of recent meetings. We will keep this website updated so that visitors can learn of progress and join general and trait-specific mailing lists. For those of you who will be at the Eucarpia Fruit Breeding Conference in Zaragoza in a couple of weeks, an ad hoc gathering will be held. In an international context, we will discuss standardized phenotyping in each of the four categories of quality, pest and disease resistance, abiotic stress resistance/adaptation, and productivity (including flowering and plant architecture).We will seek to create subgroups of interested people to continue discussions in each category into the future. The time and place of this meeting is still to be determined, but will probably be after the RosIGI meeting on Monday 17 September. The agenda will be posted on the Standardized Phenotyping website. Anyone who is interested in this topic, whether or not they will be in Zaragoza, is also welcome to contact Gayle Volk (gayle.volk(a)ars.usda.gov) or Cameron Peace (cpeace(a)wsu.edu).

18 years, 5 months

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FW: Ros IGI meeting at EUCARPIA

by Main, Doreen

--------------------------------------------------------------------- Dorrie Main, PhD Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 --------------------------------------------------------------------- ________________________________ From: Sue Gardiner [mailto:SGardiner@hortresearch.co.nz] Sent: Sun 9/2/2007 4:48 PM To: lewersk(a)ba.ars.usda.gov; jasper(a)cil.biotech.uwc.ac.za; Korban(a)uiuc.edu; Olmstead, James Winston; riccardo.velasco(a)iasma.it; angela.baldo(a)ars.usda.gov; mvandyke(a)uwc.ac.za; Emily Buck; Jean-Marc Celton; iezzoni(a)msu.edu; foucher(a)angers.inra.fr; mam262(a)cornell.edu; eb31(a)cornell.edu; slovinj(a)ba.ars.usda.gov; aorellana(a)unab.cl; d-byrne(a)tamu.edu; pere.arus(a)irta.es; toshiya(a)affrc.go.jp; Sue Gardiner; tom.davis(a)unh.edu; Main, Doreen; tzhebe(a)clemson.edu; ann.callahan(a)ars.usda.gov; Peace, Cameron; chris.dardick(a)ars.usda.gov; werner.howad(a)irta.es; jill.bushakra(a)driscolls.com; sjung(a)clemson.edu; decroocq(a)bordeaux.inra.fr; Dhingra, Amit; sosinski(a)ncsu.edu; RFolta(a)ufl.edu; ebenezer(a)uckac.edu; gvolk(a)lamar.colostate.edu; cornb(a)ars.grin.gov; deparfitt(a)ucdavis.edu; FBLiss(a)dcn.org; gvansickle(a)caltreefruit.com; mcferson(a)treefruitresearch.com; michael.wisniewski(a)ars.usda.gov; jay.norelli(a)ars.usda.gov; hsa1(a)cornell.edu; csimon(a)ars-grin.gov; zhu(a)tfrl.ars.usda.gov; skb3(a)cornell.edu; gennaro.fazio(a)ars.usda.gov Cc: rsocias(a)aragon.es; Richard Volz; Allan White; Vincent Bus; Roger Hellens; Andrew Granger Subject: Ros IGI meeting at EUCARPIA Hi all, - There will be a meeting of RosIGI (International Rosaceae Genomics Initiative) at the Zaragoza 12th EUCAPIA Symposium on Fruit Breeding and Genetics on Mon 17th September. I have been advised by the programme organizers that the advertized meetings that afternoon will take place in sequence rather than simultaneously; this is a great relief as most of us need to attend more than one meeting. - I attach the minutes of our previous meeting at PAG XV in January. I am sorry I did not distribute these earlier, they got buried under other events. I am addressing this email initially to you who attended, and will distribute the message more widely through GDR. My apologies to those who get the message twice - if you know folk who would be interested and don't appear to be on either lists please forward the message to them. We need to make up an agenda of the most urgent items - we are unlikely to have more than an hour for our meeting! Suggestions so far include: White Paper Brief updates on sequencing programmes News on RGC4 Please send items to me by the end of this week, so I can send the agenda out before I leave NZ for Spain. See you in Spain! Sue PS It is raining most days here and I can't wait to get to Spain, it is my very first visit there. ___________________________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. ___________________________________________________________________

18 years, 5 months

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Fwd: RGC4 info

by Sook Jung

Dear colleagues, I'm forwarding the message that announces the website for the RGC4 conference. www.rgc4.cl It's also linked from the GDR home page. Best, Sook Jung ---------- Forwarded message ---------- From: Ariel Orellana López <aorellana(a)unab.cl> Date: Aug 24, 2007 11:13 AM Subject: RGC4 info To: sjung(a)clemson.edu Dear Sook: There is new information about the RGC4 conference at www.rgc4.cl web site. I would appreciate if you can re-send this email to all the people in the GDR mailing list. Thanks Best wishes Ariel Orellana

18 years, 5 months

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Fruit cortex and fruit core

by Chih-Wei Tung

Hi, Rosaceae community, I have a question regarding to the fruit structure terminology which are used in GDR database "genebank apple cDNA library" (http:// www.bioinfo.wsu.edu/gdr/projects/malus/unigeneV3/ malus_librarySummary.shtml). Please help me to define or clarify the following terms, I will add them either as new ontology terms or synonyms to the existing plant ontology based on your answers fruit cortex -> is it the same as flesh or mesocarp? are these three terms used interchangeable? fruit core -> is this the tissue in the center of the fruit as seen in http://www.uq.edu.au/_School_Science_Lessons/5.6FruitPome.GIF? does it include seeds? what's the definition? Currently Plant Ontology database has "fruit placenta: a more or less localized region within a fruit to which seeds are attached", can "fruit placenta" be a synonym to "fruit core"? Your opinion and comments are sincerely appreciated! Thank you, Chih-Wei Tung Plant Ontology Consortium Cornell University Ithaca, NY www.plantontology.org

18 years, 5 months

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4th Rosaceae Genomics Conference

by Gholamreza Rabiei

Dear Dr Sook Jung, This is Gholamreza Rabiei -PhD student- at the University of New England (Australia). I would like to attend the 4th International Rosaceae Genomics Conference, but couldn't find any information on how to register and costs involved. Unfortunately the web page for the conference is not working (http://www.rgc4.cl/apache2-default). It is greatly appreciated if you could kindly provide me with some information in this regard. Best regards, Gholamreza Rabiei

18 years, 6 months

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Re: [GDR] RE: Rosaceae Descriptor meeting at ASHS

by Tom Davis

To all, for comment: The descriptor "ploidy" should be defined as "number of chromosome sets", not as "number of chromosomes". I suggest inclusion or substitution of a descriptor called "chromosome number". This number should be expressed in a manner that expresses ploidy as well as chromosome number; For the octoploid strawberry, the chromosome number should be expressed as 2n = 8x = 56, in which the term "2n" indicates a "sporophytic" number as opposed to a "gametophytic (n) number, the term "x" denotes the number of chromosomes in a basic set (x=7 for Fragaria), and the coefficient preceding the x denotes the number of chromosome sets (i.e., the ploidy, which in this case is 8). Tom Davis Professor, Plant Biology/Genetics Department of Plant Biology Rudman Hall University of New Hampshire Durham, NH USA Phone: 603-862-3217 Fax: 603-862-3784 e-mail: tom.davis(a)unh.edu At 12:15 PM 7/26/2007, Volk, Gayle wrote: ><<rosaceaedescriptorlists.xls>> <<Descriptors Lists for RosaceaeNPGS.doc>> > >I apologize for sending a file earlier this week that had some errors in >it. The descriptor classes (column E) of the former version were >misaligned with the descriptor names. The attached file has column E >deleted and has been formatted for easier use and printing. It also has a >typo of NAGS switched to NPGS in the Source column. The NPGS descriptors >are those described by the National Plant Germplasm System Crop Germplasm >Committees and information on the descriptor classes is available on the >GRIN website (For apple: ><http://www.ars-grin.gov/cgi-bin/npgs/html/desclist.pl?115>http://www.ars-grin.gov/cgi-bin/npgs/html/desclist.pl?115 >and see attached file for links) The Bioversity descriptors are available >online at the Bioversity website ><http://www.bioversityinternational.org/Publications/pubseries.asp?ID_SERIE=…>http://www.bioversityinternational.org/Publications/pubseries.asp?ID_SERIE=… >and the Eurisco descriptors are available online as well. > >Apple: ><http://www.nfc.u-net.com/mindes1.htm>http://www.nfc.u-net.com/mindes1.htm >Prunus: ><http://www.bordeaux.inra.fr/urefv/base/>http://www.bordeaux.inra.fr/urefv/base/ > >Pear: ><http://pyrus.cra.wallonie.be/specific.php>http://pyrus.cra.wallonie.be/specific.php > > >If other groups have descriptor sets that could be included in the excel >spreadsheet, please e-mail information to me. I'd be happy to add them. > >--Gayle > >Gayle Volk >USDA-ARS-NCGRP >1111 S Mason St. >Ft Collins, CO 80521 >970-495-3205 >_____________________________________________ >From: Volk, Gayle >Sent: Tuesday, July 24, 2007 6:32 PM >To: 'gdr-list(a)bioinfo.wsu.edu' >Subject: Rosaceae Descriptor meeting at ASHS > >We held a meeting among folks interested in developing (or learning more >about) some descriptors across Rosacaea at the ASHS meetings last >week. I've attached the minutes from that meeting (thanks to Jim McFerson >and Nahla Bassil for their comments), as well as some associated >spreadsheets. I realize that not all members of the Rosaceae genomics >community may be interested in receiving e-mail on the descriptor sets in >the future. We'll continue future discussions among the lists of people >listed in the minutes (attendees as well as those who couldn't make it at >that meeting). Please let me know if you would like to be added to that >mailing list. > >General background and a future direction for deciding upon Rosaceae >descriptors was discussed at the meeting last week (see attached >minutes). The next step is to brainstorm sets of descriptors from the >major classes of interest in breeding/research programs across Rosaceae: >1) disease, 2) quality, 3) yield, 4) abiotic stress. We ask that anyone >interested come up with 3-7 descriptors in one or more of the 4 categories >that could be of interest across at least 2 genera within >Rosaceae. Eventually, we'll have to scale things to make them relative >within the genera (i.e. raw data for fruit weight as well as weight >relative to a standard) and if you'd like to comment on possible ways to >accomplish this, then please do. I'll compile a list of all the ideas we >receive and then forward it to those interested being on the mailing >lists. If you have any questions, please feel free to contact me (e-mail >is best since I'll be on travel during much of the next month). I'd like >to receive a first draft of ideas by August 10th so we can have the >compiled list available for discussion at the next descriptor meeting to >be held during the Portland, OR Fireblight meetings on August 13. > >I look forward to hearing from you. > << File: Rosaceae Descriptors for GRIN7-17-07.doc >> << File: > Descriptor classes.xls >> << File: trait ontologies.xls >> << File: > rosaceaedescriptorlists.xls >> > >Gayle > >Gayle Volk >USDA-ARS-NCGRP >1111 S Mason St. >Ft Collins, CO 80521 >970-495-3205 > > >_______________________________________________ >Main Bioinformatics Laboratory >GDR-LIST mailing list >GDR-LIST(a)bioinfo.wsu.edu

18 years, 6 months

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RE: Rosaceae Descriptor meeting at ASHS

by Volk, Gayle

<<rosaceaedescriptorlists.xls>> <<Descriptors Lists for RosaceaeNPGS.doc>> I apologize for sending a file earlier this week that had some errors in it. The descriptor classes (column E) of the former version were misaligned with the descriptor names. The attached file has column E deleted and has been formatted for easier use and printing. It also has a typo of NAGS switched to NPGS in the Source column. The NPGS descriptors are those described by the National Plant Germplasm System Crop Germplasm Committees and information on the descriptor classes is available on the GRIN website (For apple: http://www.ars-grin.gov/cgi-bin/npgs/html/desclist.pl?115 and see attached file for links) The Bioversity descriptors are available online at the Bioversity website http://www.bioversityinternational.org/Publications/pubseries.asp?ID_SER IE=13 and the Eurisco descriptors are available online as well. Apple: http://www.nfc.u-net.com/mindes1.htm Prunus: http://www.bordeaux.inra.fr/urefv/base/ Pear: http://pyrus.cra.wallonie.be/specific.php If other groups have descriptor sets that could be included in the excel spreadsheet, please e-mail information to me. I'd be happy to add them. --Gayle Gayle Volk USDA-ARS-NCGRP 1111 S Mason St. Ft Collins, CO 80521 970-495-3205 > _____________________________________________ > From: Volk, Gayle > Sent: Tuesday, July 24, 2007 6:32 PM > To: 'gdr-list(a)bioinfo.wsu.edu' > Subject: Rosaceae Descriptor meeting at ASHS > > We held a meeting among folks interested in developing (or learning > more about) some descriptors across Rosacaea at the ASHS meetings last > week. I've attached the minutes from that meeting (thanks to Jim > McFerson and Nahla Bassil for their comments), as well as some > associated spreadsheets. I realize that not all members of the > Rosaceae genomics community may be interested in receiving e-mail on > the descriptor sets in the future. We'll continue future discussions > among the lists of people listed in the minutes (attendees as well as > those who couldn't make it at that meeting). Please let me know if > you would like to be added to that mailing list. > > General background and a future direction for deciding upon Rosaceae > descriptors was discussed at the meeting last week (see attached > minutes). The next step is to brainstorm sets of descriptors from the > major classes of interest in breeding/research programs across > Rosaceae: 1) disease, 2) quality, 3) yield, 4) abiotic stress. We ask > that anyone interested come up with 3-7 descriptors in one or more of > the 4 categories that could be of interest across at least 2 genera > within Rosaceae. Eventually, we'll have to scale things to make them > relative within the genera (i.e. raw data for fruit weight as well as > weight relative to a standard) and if you'd like to comment on > possible ways to accomplish this, then please do. I'll compile a list > of all the ideas we receive and then forward it to those interested > being on the mailing lists. If you have any questions, please feel > free to contact me (e-mail is best since I'll be on travel during much > of the next month). I'd like to receive a first draft of ideas by > August 10th so we can have the compiled list available for discussion > at the next descriptor meeting to be held during the Portland, OR > Fireblight meetings on August 13. > > I look forward to hearing from you. > << File: Rosaceae Descriptors for GRIN7-17-07.doc >> << File: > Descriptor classes.xls >> << File: trait ontologies.xls >> << File: > rosaceaedescriptorlists.xls >> > Gayle > > Gayle Volk > USDA-ARS-NCGRP > 1111 S Mason St. > Ft Collins, CO 80521 > 970-495-3205 >

18 years, 6 months

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Rosaceae Descriptor meeting at ASHS

by Volk, Gayle

We held a meeting among folks interested in developing (or learning more about) some descriptors across Rosacaea at the ASHS meetings last week. I've attached the minutes from that meeting (thanks to Jim McFerson and Nahla Bassil for their comments), as well as some associated spreadsheets. I realize that not all members of the Rosaceae genomics community may be interested in receiving e-mail on the descriptor sets in the future. We'll continue future discussions among the lists of people listed in the minutes (attendees as well as those who couldn't make it at that meeting). Please let me know if you would like to be added to that mailing list. General background and a future direction for deciding upon Rosaceae descriptors was discussed at the meeting last week (see attached minutes). The next step is to brainstorm sets of descriptors from the major classes of interest in breeding/research programs across Rosaceae: 1) disease, 2) quality, 3) yield, 4) abiotic stress. We ask that anyone interested come up with 3-7 descriptors in one or more of the 4 categories that could be of interest across at least 2 genera within Rosaceae. Eventually, we'll have to scale things to make them relative within the genera (i.e. raw data for fruit weight as well as weight relative to a standard) and if you'd like to comment on possible ways to accomplish this, then please do. I'll compile a list of all the ideas we receive and then forward it to those interested being on the mailing lists. If you have any questions, please feel free to contact me (e-mail is best since I'll be on travel during much of the next month). I'd like to receive a first draft of ideas by August 10th so we can have the compiled list available for discussion at the next descriptor meeting to be held during the Portland, OR Fireblight meetings on August 13. I look forward to hearing from you. <<Rosaceae Descriptors for GRIN7-17-07.doc>> <<Descriptor classes.xls>> <<trait ontologies.xls>> <<rosaceaedescriptorlists.xls>> Gayle Gayle Volk USDA-ARS-NCGRP 1111 S Mason St. Ft Collins, CO 80521 970-495-3205

18 years, 6 months

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[Fwd: FW: Phenotypes for Rosaceae]

by angela baldo

Hi Everyone, Gayle Volk had difficulty posting this message to the gdr-list, so I'm going to try forwarding it for her. Anyone who is going to ASHS in Scottsdale next week and/or is interested in phenotyping of Rosaceae by the NPGS will want to read it. Cheers, anja -------- Forwarded Message -------- > From: Volk, Gayle <Gayle.Volk(a)ARS.USDA.GOV> > To: Baldo, Angela <Angela.Baldo(a)ARS.USDA.GOV> > Subject: FW: Phenotypes for Rosaceae > Date: Tue, 10 Jul 2007 10:36:08 -0400 > > At the Rosaceae Specialty Crops planning workshop in East Lansing a > few weeks ago, I understand that there was some discussion on > developing lists of uniform descriptors across Rosaceae species. The > USDA-ARS-National Plant Germplasm System has lists of descriptors that > have been developed by crop-specific Crop Germplasm Committees > (membership information attached). There are also lists of > descriptors that have been developed through European Working Groups. > I believe there is an interest within the Rosaceae community to review > these lists of descriptors (NPGS descriptors are attached) and decide > if changes or additions are necessary. Nahla Bassil has proposed that > we have a meeting among interested researchers at the ASHS meetings in > Scottsdale next week to discuss this subject. We would appreciate > hearing from you (bassiln(a)science.oregonstate.edu; > gvolk(a)lamar.colostate.edu) if you would like to participate in this > meeting, and Nahla will set up the time and location. FYI, the annual > Prunus CGC meeting will also be held during the ASHS meetings next > week. > > We'd appreciate hearing from you by Wednesday afternoon, July 11 if > you are willing to attend a meeting next week to discuss descriptors > at ASHS. If you won't be attending the ASHS meetings, but have input > you'd like to provide, please e-mail us. We'd like to find out which > members of the Rosaceae community are interested in this topic. > > <<rose_cgc.pdf>> <<Descriptors Lists for Rosaceae.doc>> > Thanks, > Gayle Volk > > USDA-ARS > National Center for Genetic Resources Preservation > 1111 S Mason St. > Ft Collins, CO 80521 > 970-495-3205 > -- Angela M. Baldo, PHD Computational Biologist USDA, ARS Plant Genetic Resources Unit New York State Agricultural Experiment Station 630 W. North Street Geneva, NY 14456-0462 USA voice 315 787-2413 or 607 254-9413 fax 315 787-2339 or 607 254-9339 angela.baldo(a)ars.usda.gov http://www.ars.usda.gov/NAA/Geneva

18 years, 7 months

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FW: Phenotypes for Rosaceae

by Volk, Gayle

> At the Rosaceae Specialty Crops planning workshop in East Lansing a > few weeks ago, I understand that there was some discussion on > developing lists of uniform descriptors across Rosaceae species. The > USDA-ARS-National Plant Germplasm System has lists of descriptors that > have been developed by crop-specific Crop Germplasm Committees > (membership information attached). There are also lists of > descriptors that have been developed through European Working Groups. > I believe there is an interest within the Rosaceae community to review > these lists of descriptors (NPGS descriptors are attached) and decide > if changes or additions are necessary. Nahla Bassil has proposed that > we have a meeting among interested researchers at the ASHS meetings in > Scottsdale next week to discuss this subject. We would appreciate > hearing from you (bassiln(a)science.oregonstate.edu; > gvolk(a)lamar.colostate.edu) if you would like to participate in this > meeting, and Nahla will set up the time and location. FYI, the annual > Prunus CGC meeting will also be held during the ASHS meetings next > week. > > We'd appreciate hearing from you by Wednesday afternoon, July 11 if > you are willing to attend a meeting next week to discuss descriptors > at ASHS. If you won't be attending the ASHS meetings, but have input > you'd like to provide, please e-mail us. We'd like to find out which > members of the Rosaceae community are interested in this topic. > <<rose_cgc.pdf>> <<Descriptors Lists for Rosaceae.doc>> > Thanks, > Gayle Volk > > USDA-ARS > National Center for Genetic Resources Preservation > 1111 S Mason St. > Ft Collins, CO 80521 > 970-495-3205

18 years, 7 months

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1st announcement of the International Rose Genomics meeting

by Fabrice Foucher

Dear Rose researchers, We are pleased to invite you to *the first International Rose Genomics meeting in Angers (France) from the 11th to 13th of December 2007*. The aim of the meeting is to provide a setting where all private and public researchers involved in rose breeding, genetics, and genomics interchange information and, set priorities in the emerging area of rose genomics to best direct our efforts to improve rose breeding. The development of rose genomics needs an international effort from public and private groups to launch collaborations for the creation of international initiatives for funding projects. You will find all the information concerning the meeting on the the following website : http://colloque.inra.fr/rosegenomics2007. We asked you to preregister on line (with no payment) in order to evaluate the number of participants. The registration (with payment) will be opened later in September. We encourage you to submit an abstract for selection to an oral presentation. Feel free to circulate this 1st announcement to your colleagues and collaborators involved in rose breeding, genetics and genomics. If you have any questions, do not hesitate to contact the organization committee (rose.genomics2007(a)angers.inra.fr) We hope to see you in Angers. Fabrice Foucher For the organization committee.

18 years, 7 months

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NPGS Resources for Rosaceae

by angela baldo

Hi Everyone, Gayle Volk at the USDA-ARS National Center for Genetic Resources Preservation in Ft. Collins, CO has put together some resources that we might find helpful: NPGSRosaceae.doc summarizing recent changes in the USDA-ARS National Plant Germplasm System "NPGS" (genotyping Rosaceae, and improvements to the Genetic Resources Information Network "GRIN") Rosaceae inventory.xls A summary of the Malus, Pyrus, Fragaria, Prunus, Rubus, and Rosa accessions held in the germplasm system Descriptors Lists for Rosaceae.doc A large file with links in it, listing all the morphological descriptors for which there is information in GRIN. Feel free to contact Gayle directly if you have any questions, comments, or suggestions; or if you'll be in Michigan this week, I can try and clarify things. Cheers, anja -- Angela M. Baldo, PHD Computational Biologist USDA, ARS Plant Genetic Resources Unit & Grape Genetics Research Unit New York State Agricultural Experiment Station 630 W. North Street Geneva, NY 14456-0462 USA voice 315 787-2413 or 607 254-9413 fax 315 787-2339 or 607 254-9339 angela.baldo(a)ars.usda.gov http://www.ars.usda.gov/NAA/Geneva

18 years, 8 months

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CAP core idea solicitation

by Peace,Cameron

***Sorry to those of you who have already received this message - this time it is being sent to a wider audience*** Dear Rosaceae crops genomics, genetics, and breeding community, To help focus our community during the upcoming Rosaceae Specialty Crops Planning Workshop (RSCPW - say three times fast!) in East Lansing, June 22-23, we solicit your input for core ideas for a full CAP proposal to USDA-NRI. Note that this is a US funding opportunity and must have clear outcomes for the US. However, international collaborations are welcome, especially those that leverage existing resources and expertise. The Workshop foremost will be a community-building effort, bringing together a diverse range of stakeholders in the future of Rosaceae crop improvement. At the same time, we will seek to develop strategies for practical application of genomics to provide positive outcomes for industry and society. One channel for such strategies is through individual project proposals that are aligned with community objectives (White Paper and Roadmap). Another is on a broader scale via an Applied Plant Genomics Coordinated Agricultural Project (CAP) through the USDA-NRI. To show development as a community, and to have any chance of getting funded at the CAP level, we need consensus - we all need to get behind something! A CAP project will involve many institutions across the US and abroad. No CAP proposal will cover all of our needs - that's a reality that our diversity entails. But any funded RosCAP would be a massive boost to us all, and a stepping stone to so much else we want to achieve. In the end, a successful RosCAP requires that we all get behind a single idea to spearhead applied genomics in Rosaceae. Our workshop duration is short, and our experience, expertise, and opinions diverse. The RSCPW steering committee agrees that would be useful if we entered the meeting with some ideas for CAP proposals in hand. This would save time during the proceedings and give all participants the chance to consider these various ideas prior to the workshop and to prepare for further discussion. It enables active community members to be active, requires nothing further from less active members, and will provide solid foundations to build a CAP proposal with wide community involvement. We do not intend to put the cart before the horse. It is understood that before, during, and after the workshop we will be discussing obstacles and opportunities for applied genomics in Rosaceae. Some of you will raise valid points that have never before been thought of by the rest of us. All of this will be considered, and we must keep our ideas open for such input. However, we increase our chances of coming out with a clear strategy and make greater gain if we start the workshop with some core project ideas in mind - circulated widely before the workshop, to be discussed during the workshop. Details for core idea submission: The outlines should be short - 2 pages maximum. To enable dissemination to the rest of the community before the workshop, they must be submitted by Monday 11 June. Submit to the RSCPW core idea coordinator, Cameron Peace via email: cpeace(a)wsu.edu Use the following headings: Working title Objective(s) Synopsis Alignment with US White Paper and Roadmap Supporters You should consult the USDA-NRI 2007 RFA (http://www.csrees.usda.gov/funding/rfas/pdfs/07_nri.pdf, pp34-39) for the scope and particulars of a CAP proposal, and read up on successfully funded CAPs. White Paper, March 2006: http://www.bioinfo.wsu.edu/gdr/community/rosexec/RosWP_March_2006.doc Roadmap, February 2007: http://www.bioinfo.wsu.edu/gdr/community/rosexec/documents/USRosEXEC_Roa dmap_0207.doc I don't see why individual people can't support multiple core ideas at this stage, so if you think of or hear of more than one potentially useful core idea, put your name down on each. But remember that in the end, there can be only one CAP proposal from our community. The expectation of the RSCPW steering committee is that ideas will be hatched, discussed among colleagues to refine details and garner support, written in the above format, and submitted by Monday June 11. Shortly thereafter, I will distribute your core ideas, on behalf of the RSCPW steering committee, to Rosaceae participants of the workshop, so that each idea can be considered and discussed by this wider audience in the week before the workshop, and then used as foci and jumping-off points for discussion during the workshop, both informally and formally. We can refine, amalgamate, or discard ideas as we go. During Day 1 of the workshop, speakers may refer directly to the pros or cons of a particular core idea. During Day 2, our discussions will be more focused and can directly refer to the merits of these suggested core ideas, putting us ahead in developing our strategic plan and implementation plan. This will greatly help us achieve Workshop Deliverables 2 and 3. Workshop deliverables: 1) We will develop a final workshop report to summarize the outcomes of the discussions... 2) A strategic plan for development of "science to the marketplace" for Rosaceous crops to guide individual future funding efforts in the community. 3) A community framework for a CAP in Rosaceae that can be translated into proposals to relevant agencies. If you have any other comments/ ideas/suggestions for workshop consideration that are not formalized as a core idea in the above format, you are strongly encouraged to submit them in the web form hosted on the GDR (http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_crops_planning_workshop_inpu t_form.cgi). These comments will be compiled and made available as part of the workshop packet that will be disseminated prior to the workshop, and presented at the workshop within planned discussion sessions. Cameron Peace, on behalf of the RSCPW steering committee

18 years, 8 months

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RE: [GDR] GDR Renewal

by Considine, Michael

Dear All, I am deeply disappointed with this development (or rather lack of it!). I had not yet attended any GDR meetings or formally collaborated with you but had been working towards that point. We have a relatively successful apple breeding program here in Western Australia (Cripps Pink, ie Pink Lady and Cripps Red, ie Sundowner among the releases). Although very much based on conventional breeding, we are developing molecular capacity and hoping to develop international collaboration. The withdrawal of funding for GDR is a setback for us all. Kind regards, Mick Dr Michael Considine Research Scientist Horticulture Department of Agriculture WA 3 Baron-Hay Crt, South Perth, WA, 6151 alt email. mickcons(a)cyllene.uwa.edu.au ph. +61 8 9368 3209 fax. +61 8 9368 2958 -----Original Message----- From: gdr-list-bounces(a)bioinfo.wsu.edu [mailto:gdr-list-bounces@bioinfo.wsu.edu] On Behalf Of riccardo velasco Sent: Sunday, 20 May 2007 1:28 AM To: Main, Doreen; gdr-list(a)bioinfo.wsu.edu Subject: Re: [GDR] GDR Renewal Dear Doreen although I am just arrived in the Rosaceae world I can say you have done one of the best works ever seen. I hope things will go better again soon, in between thanks a lot for your efforts and nice collaboration initiative. hopefully we will meet soon in Zaragoza, I will keep you and the community informed about the progress on apple genome. best regards --- "Main, Doreen" <dorrie(a)wsu.edu> ha scritto: > Hi Folks, > > NSF are unable to support a renewal for GDR this > year although a small supplementary award to the > original grant may be possible. While it is very > dissapointing, we will continue to do what we can > while we pursue other sources of funding but please > be aware we don't have any resources available to us > at the current time. > > You have been a really great community to work with > and we appreciate all your support as we have built > the database. > > Cheers > > > Dorrie, Sook and Bert > > > --------------------------------------------------------------------- > Dorrie Main, PhD > Associate Professor of Bioinformatics > Center for Integrated Biotechnology > Dept of Horticulture and Landscape Architecture > Washington State University > 45 Johnson Hall, Pullman, WA 99164-6414 > Email: dorrie(a)wsu.edu > Tel: (509) 335 2774 > Fax: (509) 335 8690 > --------------------------------------------------------------------- > > _______________________________________________ > Main Bioinformatics Laboratory > GDR-LIST mailing list > GDR-LIST(a)bioinfo.wsu.edu ___________________________________ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html _______________________________________________ Main Bioinformatics Laboratory GDR-LIST mailing list GDR-LIST(a)bioinfo.wsu.edu This e-mail and files transmitted with it are privileged and confidential information intended for the use of the addressee. The confidentiality and/or privilege in this e-mail is not waived, lost or destroyed if it has been transmitted to you in error. If you received this e-mail in error you must (a) not disseminate, copy or take any action in reliance on it; (b) please notify the Department of Agriculture and Food, WA immediately by return e-mail to the sender; (c) please delete the original e-mail. This email has been successfully scanned by McAfee Anti-Virus software. Department of Agriculture and Food WA

18 years, 8 months

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GDR Renewal

by Main, Doreen

Hi Folks, NSF are unable to support a renewal for GDR this year although a small supplementary award to the original grant may be possible. While it is very dissapointing, we will continue to do what we can while we pursue other sources of funding but please be aware we don't have any resources available to us at the current time. You have been a really great community to work with and we appreciate all your support as we have built the database. Cheers Dorrie, Sook and Bert --------------------------------------------------------------------- Dorrie Main, PhD Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 ---------------------------------------------------------------------

18 years, 9 months

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RE: [GDR] GDR Renewal

by Arús, Pere

Dear Dorrie, Sook, Bert, This is really bad news. I think that we cannot afford to loose such a useful resource, that would be a clear step back in the progress of Rosaceae genomics. We have to start thinking of ways to keep the GDR going. Thanks for all your efforts and for having made available to us this useful tool. Best regards, Pere ________________________________ De: gdr-list-bounces(a)bioinfo.wsu.edu [mailto:gdr-list-bounces@bioinfo.wsu.edu] En nom de Main, Doreen Enviat: divendres, 18 / maig / 2007 21:07 Per a: gdr-list(a)bioinfo.wsu.edu Tema: [GDR] GDR Renewal Hi Folks, NSF are unable to support a renewal for GDR this year although a small supplementary award to the original grant may be possible. While it is very dissapointing, we will continue to do what we can while we pursue other sources of funding but please be aware we don't have any resources available to us at the current time. You have been a really great community to work with and we appreciate all your support as we have built the database. Cheers Dorrie, Sook and Bert --------------------------------------------------------------------- Dorrie Main, PhD Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 ---------------------------------------------------------------------

18 years, 9 months

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Two postdoctoral opportunities (in apple functional genomics and rose architecture)

by Sook Jung

Dear colleagues, I am forwarding the advertisement for two postdoctoral opportunities: one in apple functional genomics at USDA/Washington State University and the other in garden rose architecture at INRA, France. Please check GDR site for details. http://www.bioinfo.wsu.edu/gdr/community/employment/ Best, Sook

18 years, 9 months

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4th Rosaceae Genomics Conference

by Sook Jung

4th Rosaceae Genomics Conference First Announcement: With the recent news regarding the genome sequencing of members of the Rosaceae family, the next few years promise to be very fruitful and exciting times. With the hope of sharing information associated these and other exciting advances, we invite you to join us at the 4th International Rosaceae Genomics Conference to be held in CHILE. The 4th RGC should be a turning point in Rosaceae Genomics research and will help us to organize our international efforts. We look forward to seeing all of you at this meeting so that we can discuss the scientific advances as well as enjoy what Chile has to offer. Please join us at the 4th International Rosaceae Genomics Conference in Pucon, Chile. Date of Conference 16-19 March, 2008 Venue: Gran Hotel Pucon, Pucon, Chile Abstract Title Due: October 31, 2007 Abstract Due: December 31, 2007 Acceptance of presentation as oral or poster: February 1, 2008 Early bird registration close February 15, 2008 We look forward to see you in Chile!!! Saludos, Organizing Committee Lee Meisel Eliseo Campos Ariel Orellana Chair of the Scientific Committee Herman Silva

18 years, 11 months

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Ontology development for Rosaceae

by Sook Jung

Dear colleagues, GDR will be trying to more actively incorporate ontology terms to describe traits/QTLs and also to further develop the terms required for Rosaceae, in collaboration with Plant Ontology Consortium (www.plantontology.org) and gramene. Inputs from researchers like you will be of great help for this effort, so we'd appreciate if you can share your expertise in this effort. Below is the excerpt from an email sent by Dr. Chih-Wei Tung, a POC curator. "To start this collaboration, POC researchers encouraged Rosaceae researchers to browse and search current plant ontology ( www.plantontology.org/amigo/go.cgi), as well as trait ontology ( www.gramene.org/db/ontology/search_term?id=TO:0000387), your feedback is very important for us to know what type of terms are missing or what types of terms can be modified or add as synonyms to existing ontologies, these are the information we'd really like to know from experts in Roseaceae community. If you know of any references (books, websites, etc.) which can helps us to understand the morphology, developmental stage, as well as phenotypes of Rosaceae, please share with us, this will serve as a starting point for POC curators to be familiar with these two families and facilitate us to curate new terms when needed. Thank you so much! " You can post your opinions in GDR mailing list (gdr-list(a)bioinfo.wsu.edu) so that we can share and discuss the suggestion. If needed, we can make a separate mailing list for this purpose. Thank you, Sook Jung

19 years

1
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GDR Newsletter No. 6

by Main, Doreen

Dear GDR Users; Please find attached the latest GDR newsletter. Updates and future plans for GDR will be presented at the Fruit and Nut Workshop at PAG and Dorrie and Sook will be at PAG to answer any questions you may have. As always your support of GDR and your feedback is much appreciated. Cheers Dorrie --------------------------------------------------------------------- Dr Dorrie Main Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 ---------------------------------------------------------------------

19 years, 1 month

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PAG CSREES-NRI Rosaceae Awards Updates and Strategic Planning Session location Information

by Main, Doreen

The CSREES-NRI Rosaceae awards updates and strategic planning session will be held on Friday January 12, from 6 to 10 pm in the Windsor Rose Room (Located on the 9th floor of the Regency Tower). It is an open meeting. EARLIER EMAIL INFORMATION To Rosaceae Community Members, At PAG on the evening of 12 January 2007 the recipents of the CSREES-NRI Rosaceae Awards will give short updates of their projects. Following these presentations, we have been asked to engage in a Strategic Planning session. This session will be guided by three questions provided to us by Ed Kaliekau. In preparation for this session, Kevin Folta and I (on behalf of RosEXEC) and three volunteers (Carole Bassett, Cameron Peace and Schuylar Korban) have developed the attached outline which we hope will help facilitate this discussion. For you review, we have provided the outline in two forms, one short 2 page version and one longer version that matches the short version but is more developed. We would appreciate your reading over the outline(s) we have prepared and getting back to us with your comments, alterations, etc, prior to the 12th. Thank you so much for your time. We look forward to hearing from you and meeting with you later this week. Best regards, Amy

19 years, 1 month

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RosEXEC Meeting at PAG

by Main, Doreen

Dear Rosaceae Community, The next meeting of the RosEXEC will be held on Sunday, January 14, 2006, 8-10 AM in the Town and Country Room of at the Town and Country Resort during the Plant Animal Genome XV Conference. This is an open meeting and your attendance and input are encouraged. We are in the process of generating an agenda for the meeting. Please forward any business items as soon as possible to me at kfolta(a)ifas.ufl.edu . Thank you, see you there. Kevin Folta

19 years, 1 month

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US RosEXEC Elections Voting Reminder

by Main, Doreen

RosEXEC ELECTIONS The US Rosaceae Genomics, Genetics, & Breeding Executive Committee (RosEXEC) will be electing five new members to replace its five outgoing members prior to PAG15. RosEXEC was organized in 2006 to serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics, and breeding community. We have four objectives: 1. Define research priorities based on input from the industry and the research community 2. Foster scientific interaction and dynamic research teams 3. Promote research priorities 4. Coordinate educational efforts from the research community to the industry and the public A list of the existing USRosEXEC members can be found on GDR at http://www.bioinfo.wsu.edu/gdr/community/rosexec/membership/index.shtml Elections will be held electronically via the GDR at http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for… The process is open to Rosaceae researchers currently based in the U.S., regardless of citizenship. Only one vote can be cast per candidate. Please strive to represent the diversity of our community by electing candidates from various crop interests, institutional affiliation, and geographic location. The US RosEXEC Membership Committee has suggested some candidates on the voting form posted on the GDR at http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for… but we urge interested community members to nominate other qualified candidates (also can be done via the voting page) or direct questions to Jim McFerson (mcferson(a)treefruitresearch.com <mailto:mcferson@treefruitresearch.com> ). Outgoing RosEXEC members are eligible for re-election to a new three year term. Please note that you can also nominate and vote on up to 4 members as international liasons for the US RosEXEC. If you have any problems using the voting page, please email Dorrie Main (dorrie(a)wsu.edu). The deadline for voting is 13 Jan 2007, 5pm PST. New members will be selected by vote totals and will serve three year terms. RosEXEC meets in person at the PAG and holds quarterly teleconferences. Amy Iezzoni is the outgoing and Kevin Folta is the incoming Chair. We will be meeting on 14 Jan, 2007, 8.00 am to 10.00 am at the XV PAG Conference, San Diego, USA. For more information see http://www.bioinfo.wsu.edu/gdr/community/rosexec/ Jim McFerson RosEXEC Membership Committee

19 years, 1 month

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Notice of Rosaceae Strategic Planning Session at PAG and Prepared Documents for community comments

by Main, Doreen

To Rosaceae Community Members, At PAG on the evening of 12 January 2007 the recipents of the CSREES-NRI Rosaceae Awards will give short updates of their projects. Following these presentations, we have been asked to engage in a Strategic Planning session. This session will be guided by three questions provided to us by Ed Kaliekau. In preparation for this session, Kevin Folta and I (on behalf of RosEXEC) and three volunteers (Carole Bassett, Cameron Peace and Schuylar Korban) have developed the attached outline which we hope will help facilitate this discussion. For you review, we have provided links via GDR to the outline in two forms, one short 2 page version <http://www.bioinfo.wsu.edu/gdr/community/rosexec/documents/GENERAL_DISCUSSI…> and one longer version <http://www.bioinfo.wsu.edu/gdr/community/rosexec/documents/GENERAL_DISCUSSI…> that matches the short version but is more developed. These links are also available via the GDR home page. (http://www.rosaceae.org). We would appreciate your reading over the outline(s) we have prepared and getting back to us with your comments, alterations, etc, prior to the 12th. Thank you so much for your time. We look forward to hearing from you and meeting with you later this week. Best regards, Amy

19 years, 1 month

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Call for Applications for HortResearch Travel Awards for USA-New Zealand Rosaceae Genomics Partnership Initiative

by Main, Doreen

Call for Applications for HortResearch Travel Awards for USA-New Zealand Rosaceae Genomics Partnership Initiative One of the recommendations from the NSF / MoRSTUSA - New Zealand Rosaceae Genomics Partnership Workshop, held in New Zealand in May 2006, following the 3 rd International Rosaceae Genomics Conference, was to encourage the exchange of young researchers between USA and New Zealand. In response to this, HortResearch offers partial funding to 2 young scientists currently working in USA laboratories, to work alongside genomics researchers in their laboratories in New Zealand. HortResearch is best-known for its apple genomics research and has developing programmes in Prunus, Rubus and Pyrus. The Fruit Genomics Group at HortResearch has an extensive collection of ESTs from apple, as well as from kiwifruit, blueberry and avocado. The major bioinformatics capability is complemented by re-sequencing, EST cloning, transient and stable transformation (apple, kiwifruit, tobacco and Arabidopsis), to identify the function of candidate genes , and also oligo arrays, proteomic and metabolomics platforms. Key horticultural production traits focus on bud break and flowering, while consumer trait research focuses on colour and health, as well as fruit texture. There is particular interest in discovering the regulatory genes (transcription factors) that may coordinate these complex horticultural traits. Research areas offering placements include: 'High throughput mapping /disease, tree and quality traits' - Sue Gardiner; 'Overgos' - Elena Hilario; 'Disease resistance cloning' - Erik Rikkerink; 'Microarrays' - Robert Schaffer; 'In situ hybridisation and immunolocalization' - Toshi Foster; 'Transient expression' - Roger Hellens; 'Transgenics' - Andy Allan; 'Protein expression; enzymology, proteomics' - William Laing; 'Breeding' - Vincent Bus, Richard Volz. Descriptions of team activities can be obtained from SGardiner(a)hortresearch.co.nz <mailto:SGardiner@hortresearch.co.nz> . General information on HortResearch can be found at http://www.hortresearch.co.nz <http://www.hortresearch.co.nz/> Applications are being solicited from young scientists (graduate students and postdocs or postdoc equivalents) working in US institutions involved in research in Rosaceae genomics, for funding of NZD 5000 plus bench fees to enable them to spend up to 1 month working with HortResearch Genomics research teams. Applications for these awards should be sent by e-mail to: SGardiner(a)hortresearch.co.nz <mailto:SGardiner@hortresearch.co.nz> by Friday 2 nd February 2007. Applications must include a cv and a letter from the applicant outlining the benefits of the proposed research visit to themselves and to Rosaceae genomics research in both the US and New Zealand. A letter of support from your advisor / supervisor must also be included. Applications will be evaluated by a screening committee comprised of NZ and US scientists. Priority will be given to applicants who can demonstrate that this opportunity will directly benefit their research experience in genomics of the Rosaceae. Minority applicants are encouraged to apply. Sue Gardiner will be available at PAG XV for discussions about the Travel Awards, along with Elena Hilario, Emily Buck and Jean-Marc Celton, also from HortResearch.

19 years, 1 month

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US RosEXEC elections

by Main, Doreen

RosEXEC ELECTIONS The US Rosaceae Genomics, Genetics, & Breeding Executive Committee (RosEXEC) will be electing five new members to replace its five outgoing members prior to PAG15. RosEXEC was organized in 2006 to serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics, and breeding community. We have four objectives: 1. Define research priorities based on input from the industry and the research community 2. Foster scientific interaction and dynamic research teams 3. Promote research priorities 4. Coordinate educational efforts from the research community to the industry and the public A list of the existing USRosEXEC members can be found on GDR at http://www.bioinfo.wsu.edu/gdr/community/rosexec/membership/index.shtml. Elections will be held electronically via the GDR at (http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for… <http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for…> ). The process is open to Rosaceae researchers currently based in the U.S., regardless of citizenship. Only one vote can be cast per candidate. Please strive to represent the diversity of our community by electing candidates from various crop interests, institutional affiliation, and geographic location. The US RosEXEC Membership Committee has suggested some candidates on the voting form posted on the GDR (http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for… <http://www.bioinfo.wsu.edu/cgi-bin/gdr/gdr_rosexec_membership_2006_vote_for…> ), but we urge interested community members to nominate other qualified candidates (also can be done via the voting page) or direct questions to Jim McFerson (mcferson(a)treefruitresearch.com <mailto:mcferson@treefruitresearch.com> ). Outgoing RosEXEC members are eligible for re-election to a new three year term. Please note that you can also nominate and vote on up to 4 members as international liasons for the US RosEXEC. If you have any problems using the voting page, please email Dorrie Main (dorrie(a)wsu.edu). The deadline for voting is 13 Jan 2007, 5pm PST. New members will be selected by vote totals and will serve three year terms. RosEXEC meets in person at the PAG and holds quarterly teleconferences. Amy Iezzoni is the outgoing and Kevin Folta is the incoming Chair. We will be meeting on 14 Jan, 2007, 8.00 am to 10.00 am at the XV PAG Conference, San Diego, USA. For more information see http://www.bioinfo.wsu.edu/gdr/community/rosexec/ <http://www.bioinfo.wsu.edu/gdr/community/rosexec/> Jim McFerson RosEXEC Membership Committee

19 years, 1 month

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test

by Svancara Randall

test -- Randall Svancara Systems Administrator (509) 335-3623

19 years, 2 months

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(no subject)

by Gerardo Sánchez

Lic. Gerardo Sánchez Grupo Horticultura INTA - EEA San Pedro Ruta 9 km 170 2930 San Pedro, Buenos Aires, Argentina TE: 54+03329+423321 e-mail: gsanchez(a)correo.inta.gov.ar Web: www.inta.gov.ar/sanpedro/index.htm

19 years, 2 months

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Rosaceae Community Members

by Encore Events

Hi all fellow Rosaceae Community members! (My apologies if you have this already - I have 2 mailing lists.....) We have an open meeting scheduled at PAGXV in San Diego, Sunday Jan 14th 2007 from 10am -12 midday. Room to be notified. This is our first chance for a get-together since RGC3 in Napier earlier this year. Can you please let me know; 1. If you will be at this meeting - so that we can distribute any papers to you prior to the meeting. 2. Items you would like to discuss....... - I can think of our White Paper as a matter of urgency; - It would be good to have an update on the progress of RosPOP - And any information on international sequencing project plans, - Genetic marker exchanges....... - Reviews / books planned, in progress - What else is dear to you? Best wishes, Sue Gardiner, Chair, RosIGI steering committee. Dr. Susan Gardiner, Principal Scientist, Plant Gene Mapping, HortResearch, Private Bag 11030, Palmerston North, New Zealand. Telephone: +64 6 356 8080 ext. 7772 Fax: +64 6 354 6731 ______________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. ______________________________________________________

19 years, 2 months

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Associate in Research at WSU

by Dhingra, Amit

Please forward to anyone interested in your organization. Position is also listed on the GDR website. ASSOCIATE IN RESEARCH - Washington State University is seeking a highly motivated, talented, and creative scientist for a plant genomics project. Position is initially available for two years with the possibility of extension. We are looking for an individual with the demonstrated ability to primarily carry out research and manage labs. The individual will be responsible for implementing experiments as well as upkeep of lab equipment, ordering lab supplies, and training students in the lab. The successful candidate must have strong interest in plant molecular biology, bioinformatics, genomics and tissue culture. Required: a B.S. degree. Preferred: 1) a M.S. degree 2) prior experience in basic plant molecular biology techniques such as DNA extraction, cloning of PCR products, DNA sequencing, RT-PCR, plant growth, plant transformation, computer programming, and general microbial techniques; 3) ability to interact and work collaboratively with others. Application review begins immediately. Application materials includes a brief cover letter outlining interests and qualifications, curriculum vitae, transcripts, and the names and e-mail addresses of three references (please send all materials as a single PDF file). Send applications materials to Dr. Amit Dhingra, Dept. of Horticulture & Landscape Architecture, WSU, P.O. Box 646414, Pullman, WA 99164-6414. Fax: (509)335-8690; e-mail: adhingra(a)wsu.edu. AA/EE0/ADA ---------------------------------------- Amit Dhingra, Ph.D. Assistant Professor Horticulture & Landscape Architecture PO Box 646414 46 Johnson Hall Washington State University Pullman, WA 99164-6414 Phone: (509) 335-3625 Cell: (352) 246-4092 Fax: (509) 335-8690 Email: adhingra(a)wsu.edu

19 years, 3 months

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Associate in Research at WSU

by Dhingra, Amit

Please forward to anyone interested in your organization. Position is also listed on the GDR website. ASSOCIATE IN RESEARCH - Washington State University is seeking a highly motivated, talented, and creative scientist for a plant genomics project. Position is initially available for two years with the possibility of extension. We are looking for an individual with the demonstrated ability to primarily carry out research and manage labs. The individual will be responsible for implementing experiments as well as upkeep of lab equipment, ordering lab supplies, and training students in the lab. The successful candidate must have strong interest in plant molecular biology, bioinformatics, genomics and tissue culture. Required: a B.S. degree. Preferred: 1) a M.S. degree 2) prior experience in basic plant molecular biology techniques such as DNA extraction, cloning of PCR products, DNA sequencing, RT-PCR, plant growth, plant transformation, computer programming, and general microbial techniques; 3) ability to interact and work collaboratively with others. Application review begins immediately. Application materials includes a brief cover letter outlining interests and qualifications, curriculum vitae, transcripts, and the names and e-mail addresses of three references (please send all materials as a single PDF file). Send applications materials to Dr. Amit Dhingra, Dept. of Horticulture & Landscape Architecture, WSU, P.O. Box 646414, Pullman, WA 99164-6414. Fax: (509)335-8690; e-mail: adhingra(a)wsu.edu. AA/EE0/ADA ---------------------------------------- Amit Dhingra, Ph.D. Assistant Professor Horticulture & Landscape Architecture PO Box 646414 46 Johnson Hall Washington State University Pullman, WA 99164-6414 Phone: (509) 335-3625 Cell: (352) 246-4092 Fax: (509) 335-8690 Email: adhingra(a)wsu.edu

19 years, 3 months

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by MARIAJO RUBIO

19 years, 4 months

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Re: [GDR] Recommendations for Prunus QTL nomenclature

by Kimberly Lewers

Personally, I think q-Mat would be sufficient, and I like simplicity. There are other ways to address the rest of that information. Just my opinion. Kim Dr. Kim Lewers USDA/ARS Fruit Lab BARC-West, Bldg. 010A, rm. 210 10300 Baltimore Avenue Beltsville, MD 20705 office: 301-504-6768 lab: 301-504-6498 fax: 301-504-5062 e-mail: lewersk(a)ba.ars.usda.gov >>> Jim Olmstead <jwolmstead(a)wsu.edu> 09/13/06 02:17PM >>> Dear Rosaceae Community Members, During the Prunus workshop at the RGC3 Conference in New Zealand, Cameron Peace, Eben Oqundiwin and I were asked to work on developing a draft of QTL nomenclature suggestions that could be used to standardize QTL reporting within Prunus. I've attached a working document for the community as a whole to comment on. Although we have concentrated on Prunus, please note that the opportunity exists to expand these suggestions to the entire Rosaceae family. If you find this topic interesting and would like to be included in future mailings, please follow this link to the Genome Database for Rosaceae website http://www.mainlab.clemson.edu/cgi-bin/gdr/signup_ROSACEAE-QTL-LIST.cgi and sign up for the QTL topics mailing list. Once you have signed up for the mailing list, you can use the email address rosaceae-qtl-list(a)genome.clemson.edu to send mail to the subscribed group. Communications from this mailing list can then be viewed at: http://www.mainlab.clemson.edu/pipermail/rosaceae-qtl-list/ You may also address any comments and suggestions concerning this topic directly to me - you'll find the contact information below. I look forward to hearing from you! Sincerely, Jim Olmstead Cherry Breeding - Washington State University -- James Olmstead WSU-Prosser 24106 N. Bunn Rd. Prosser, WA 99350 Office: 509-786-9249 Fax: 509-786-9370 Email: jwolmstead(a)wsu.edu

19 years, 5 months

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Recommendations for Prunus QTL nomenclature

by Jim Olmstead

Dear Rosaceae Community Members, During the Prunus workshop at the RGC3 Conference in New Zealand, Cameron Peace, Eben Oqundiwin and I were asked to work on developing a draft of QTL nomenclature suggestions that could be used to standardize QTL reporting within Prunus. I've attached a working document for the community as a whole to comment on. Although we have concentrated on Prunus, please note that the opportunity exists to expand these suggestions to the entire Rosaceae family. If you find this topic interesting and would like to be included in future mailings, please follow this link to the Genome Database for Rosaceae website http://www.mainlab.clemson.edu/cgi-bin/gdr/signup_ROSACEAE-QTL-LIST.cgi and sign up for the QTL topics mailing list. Once you have signed up for the mailing list, you can use the email address rosaceae-qtl-list(a)genome.clemson.edu to send mail to the subscribed group. Communications from this mailing list can then be viewed at: http://www.mainlab.clemson.edu/pipermail/rosaceae-qtl-list/ You may also address any comments and suggestions concerning this topic directly to me - you'll find the contact information below. I look forward to hearing from you! Sincerely, Jim Olmstead Cherry Breeding - Washington State University -- James Olmstead WSU-Prosser 24106 N. Bunn Rd. Prosser, WA 99350 Office: 509-786-9249 Fax: 509-786-9370 Email: jwolmstead(a)wsu.edu

19 years, 5 months

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Recommendations for Prunus QTL nomenclature

by Jim Olmstead

Dear Rosaceae Community Members, During the Prunus workshop at the RGC3 Conference in New Zealand, Cameron Peace, Eben Oqundiwin and I were asked to work on developing a draft of QTL nomenclature suggestions that could be used to standardize QTL reporting within Prunus. I've attached a working document for the community as a whole to comment on. Although we have concentrated on Prunus, please note that the opportunity exists to expand these suggestions to the entire Rosaceae family. If you find this topic interesting and would like to be included in future mailings, please follow this link to the Genome Database for Rosaceae website http://www.mainlab.clemson.edu/cgi-bin/gdr/signup_ROSACEAE-QTL-LIST.cgi and sign up for the QTL topics mailing list. Once you have signed up for the mailing list, you can use the email address rosaceae-qtl-list(a)genome.clemson.edu to send mail to the subscribed group. Communications from this mailing list can then be viewed at: http://www.mainlab.clemson.edu/pipermail/rosaceae-qtl-list/ You may also address any comments and suggestions concerning this topic directly to me - you'll find the contact information below. I look forward to hearing from you! Sincerely, Jim Olmstead Cherry Breeding - Washington State University -- James Olmstead WSU-Prosser 24106 N. Bunn Rd. Prosser, WA 99350 Office: 509-786-9249 Fax: 509-786-9370 Email: jwolmstead(a)wsu.edu

19 years, 5 months

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GDR Newsletter May 2006

by Sook Jung

GDR Newsletter May 2006 Welcome to the fifh issue of the GDR newsletter. This newsletter is to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0506.shtml Attached is the pdf version of this newsletter. Community News White Paper The US National Rosaceae Genomic, Genetics and Breeding Executive Committee have completed the US white paper on Rosaceae Genomics. It can be downloaded from GDR and any comments can be addressed to the executive committee chair, Dr Amy Iezonni. Funding 1. A US based proposal, supported by strong international collaboration, is being submitted to the NSF Plant Genome Comparative Sequencing program in June. We are proposing to sequence the peach genome as a reference for Rosaceae, with skim sequencing of strawberry and apple, and targeted deep coverage of selected loci across multiple species. For more information contact Bryon Sosinski of NC State. 2. A US based proposal is being submitted to the NSF Networking program in June to fund a Rosaceae Informatics Network where international bioinformatics researchers will meet regularly and develop a collaborative bioinformatics infrastructure for the community database. For more information contact Dorrie Main or Bert Abbott. Conferences The 3rd International Rosaceae Genomics Conference was held March 19-22, 2006, in Napier, New Zealand. Download the conference outcomes and the abstracts from this meeting. The 4th International Rosaceae Genomics Conference is scheduled to be held in Pućon, Chile in March 2008. More details will be posted in the GDR conferences page as they become available. Employment A faculty position in plant breeding is available at the Pontificia Universidas Catolica de Chile. What's new at GDR? 1. SNPs (Single Nucleotide Polymorphisms) 2. Updates to the peach physical map 3. Updates to the Comparative Mapping Viewer CMap 4. Marker/Map data template available 5. Rosaceae Genomics White papers 6. Species page/Project page 7. New header bar 8. Community pages and mailing lists 9. New publication from GDR 10. Additions to the publication database 1. SNPs (Single Nucleotide Polymorphisms) The new Fragaria, Malus, Prunus, Pyrus, and Rosa unigenes have been searched for SNPs using the software package AutoSNP. A total of 14,801 SNPs are available to be viewed and searched, including 10426 SNPs from Malus, 3776 from Prunus, 316 from Rosa, and 283 from Fragaria. 2. Updates to the peach physical map The latest peach physical map contains 18387 BACs and 1367 contigs. Physical length of the contigs is appoximately 210-230Mb and that of the anchored contigs is 33Mb. WebFPC / WebChrom displays the peach physical map. Anchored peach BAC contigs can be accessed directly from the prunus reference TxE map from the GDR map viewer. 3. Updates to the Comparative Mapping Viewer CMap Four new maps (Apricot GxV F1 2002, Apricot LxL F2 2003, Peach AxJ 2005 and 815x903BC diploid Fragaria 2006) have been added to the genetic maps available through CMap. This now makes a total of 24 Rosaceae CMaps are available through CMap at GDR. These include: Prunus: Prunus bin map 2005, TxE almond x peach F2 2004, Myrobalan Plum x Almond- Peach hybrid 2004, GxN almond x peach F2 2001 Peach: Peach AxJ 2005, Peach PMP2 2005, Peach peach x P. ferganensis BC1 PxF 2001, Peach JxF 2004, Peach Sc x B 1998 Apricot: Apricot GxV F1 2002, Apricot LxL F2 2003 Almond: Almond FxT 2000, Almond FxB F1 1998 Sour Cherry: PcerasusEB, PcerasusRS Strawberry: FVxFN diploid Fragaria reference map, 815x903BC diploid Fragaria 2006 Apple: MNY75441-58, MNY75441-67, MWijcik_McIntosh, MRomeBeauty, MRomeBeauty_2, MWhiteAngel, MWhiteAngel_2 If you have mapping data that we can add, please contact us and we will work with you to make your data available via GDR. 4. Marker/Map data template available Efforts are underway to curate more extensive genetics data to GDR, and data templates for map/marker/trait/polymorphism/gene/QTL/Diversity are available. 5. Rosaceae Genomics White papers The US National Rosaceae Genomic, Genetics and Breeding Executive Committee have completed the US white paper on Rosaceae Genomics. They can be downloaded from GDR and any comments can be submitted to the executive committee chair, Dr Amy Iezonni. 6. Species page/Project page GDR has been reorganized to enhance navigation in the website. We have created specific species pages, under each genus where you can access all the information related to that species in GDR. Go to apple, prunus, almond, apricot, cherry, peach, rose, strawberry pages for all GDR structural genomics, functional genomics and funded project information. 7. New header bar Dropdown and left side navigation bars remodeled to enhance ease of access to GDR data. 8. Community pages and mailing lists The community page at GDR has been modified to make it easier to access the community pages of interest. In addition new International and US communication pages have been added, with new mailing lists to join (via a web form). We encourage you to join the appropriate mailing lists and use them to communicate to the community using these tools. 9. New publication from GDR Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. Sook Jung, Dorrie Main, Margaret Staton, Ilhyung Cho, Tatyana Zhebentyayeva, Pere Arus and Albert Abbott. BMC Genomics 2006, 7:81 10. Additions to the publication database The publication database on GDR now contains publication data from Agricola, the catalog of articles maintained by the National Agricultural Library. 564 relevant publications are online and can be searched by title, authors, keywords, and date published. Subscription Visit our mailing lists be added/removed to the available GDR mailing lists. Once you have registered you may use the mailing lists to send out relevant information the community and it will be stored in searchable web archives. More information is available on each page on how to use them. If you have any difficulties please contact us. The GDR mailing list. The International Rosaceae Genomics Community mailing list. The USA Rosaceae Genomics Community mailing list. Work in progress 1. Efforts to integrate more extensive map/marker data We are updating our map/marker database structure to integrate the details of molecular marker data such as primer sequences, source BAC/ESTs, produce size and much more. 2. Creation of other databases within GDR We are also creating new database modules such as gene, trait loci, QTL, polymorphism/allele, germplasm, and diversity data.

19 years, 8 months

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(no subject)

by Yanmin Zhu

19 years, 10 months

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Team Members Needed for Planning

by Sook Jung

Dear Rosaceae colleagues, I am forwarding a note from Dr. Susan Brown at Cornell about forming four sub-committees that was discussed in Rosaceae community meeting held at IFTA conference in Hershey, PA. > Team Members Needed for Planning: > There are four general theme areas of research in the Rosaceae white paper (indicated in bold text below) and we are forming four sub committees for planning purposes. Anyone with an interest in one or more of these topics, and a willingness to participate in some pre-organization work for strategic planning are encouraged to contact the scientific coordinator for each group at the Email addresses below. Please do not reply to the list serve. We would appreciate a response by March 10th. Identifying those in each core area interested in participating in the discussion will facilitate future strategic planning. The Committee is charged with figuring out how such strategic planning will happen and how it will be structured. The entire Rosaceae community will participate in the strategic planning, but this committee sets the framework. > Reducing the dependence on chemical pesticides by improving biological resistance: Herb Aldwinckle at hsa1(a)cornell.edu. > Reducing labor costs (Plant architecture): Susan Brown at skb3(a)cornell.edu. > Improving fresh and processed fruit quality, storage and safety: Abhaya Dandekar at amdandekar(a)ucdavis.edu. Improving profitability of the Rosaceae fruit industry (abiotic stress tolerance): Michael Wisniewski at mwisniew(a)afrs.ars.usda.gov.

19 years, 11 months

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Rosace Roundtable Minutes from 1-15-06 (corrected)

by Angela M. Baldo

20 years

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3rd International Rosaceae Genomics Conference - March 2006

by Encore Events

Dear All This is to remind you that, registrations for the above conference close on 15 February 2006. Registrations can be done online by visiting www.rgc3.co.nz <http://www.rgc3.co.nz/> . Please complete both sections of the registration process. If you are requiring accommodation this also needs to be reserved through us by 15 February as after that date we need to release any unallocated rooms. Please ensure that when you register you include all activities that you may wish to partake in as numbers need to be confirmed prior to conference. If you have submitted an abstract and have not registered then we remind you that you need to do so. For those who have already registered, we look forward to meeting you at Conference. Regards Sue Page Encore Events PO Box 12097, Ahuriri, Napier B 06 833 7440 F 06 833 7447 M 027 669 1345 E sue(a)encore-events.net.nz

20 years

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GDR Newsletter January 2006 pdf attachment

by Sook Jung

20 years, 1 month

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GDR Newsletter January 2006

by Sook Jung

GDR Newsletter January 2006 Welcome to the fourth issue of the GDR newsletter. This newsletter is to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0106.shtml Attached is the pdf version of this newsletter. Community News 1. Fruit and Nut Workshop, Saturday January 14, 8 am-12 pm. Plant and Animal Genome Conference XIV, San Diego, January 14-18, 2006. Conference organizer: Dr Amy Iezzoni. A Rosaceae genomics roundtable meeting will be held on Sunday January 15th, 8-10 am and the Rosaceae executive committee will meet on Sunday January 15th, 10am-12pm. 2. 3rd International Rosaceae Genomics Conference will be held in Napier, New Zealand, March 19-23, 2006. 3. The International Fruit Tree Association Annual Conference will be held in Hershey, Pennsylvania, USA, February 26-March 1, 2006 What's new at GDR? 1. Proposal to renew funding for GDR submitted to the NSF Plant Genome Program. 2. New EST libraries are available. 3. Rosaceae Unigene v2 with enhanced annotation available. 4. Prunus bin map data is available in CMap and marker search engine. 5. Enhanced SSR server now available with primer generating option. 6. More databases are available for blast/fasta sequence similarity search. 7. Data available for the three peach BACs that are completely sequenced. 8. New Roseaceae Genomics Executive Committee web page. 9. The GDR publications database now contains 242 papers relevant to Rosaceae genetics/genomics. 1. GDR Renewal Proposal Submitted to NSF Plant Genome Program In November 2005, a multi-institution proposal was submitted to the National Science Foundation Plant Genome Program to renew funding support for GDR through August 2009. The proposal if funded will significantly enhance the functionality and usefulness of GDR for the rosaceae community. If you's like more information on this proposal please contact Dorrie Main. 2. New EST libraries are available. The diploid strawberry species, Fragaria vesca, a putative genome donor to the octoploid, cultivated species (Fragaria x ananassa) is being been developed as a model system for genetic and genomic research in strawberry.Tom Davis at the University of New Hampshire, USA, has provided 2717 ESTs from the unopened flower buds of diploid strawberries. A full analysis results of his library can be viewed/downloaded from the project page and the ESTs can be queried at the EST search site. Peach (Prunus persica) represents a model species for prunus and a reference species for Rosaceae. To develop an extensive Prunus EST database for identification and cloning of genes important to fruit and tree development, Bert Abbott at Clemson University, USA, generated 8832 high-quality expressed sequence tags (ESTs) from a peach cDNA library of shoot tissue. After assembly and annotation, a putative peach unigene set consisting of 5381 ESTs was defined. Full analysis results of his library can be viewed/downloaded from the project page and the ESTs can be queried at the EST search site. 3. Rosaceae Unigene v2 with enhanced annotation available. A second version of the Rosaceae family unigene is now available. A new assembly process is being utilized; the ESTs are assembled using CAP3 within each genera (Fragaria, Malus, Prunus, Pyrus, and Rosa), and these assemblies are compiled and re-assembled together to produce the family-wide unigene. The new Rosaceae Unigene contains 72114 unigenes. Putative function has been assigned using the arabidopsis protein database and will be further expanded using the swissprot and NCBI nr protein databases. The unigenes have been analyzed for microsatellites and the results including suggested primers can be downloaded. Please see each project page (Fragaria, Malus, Prunus, Rosa and Rosaceae) to view/download all the GDR unigene data. 4. Prunus bin map is available in CMap and marker search engine. A Prunus bin map (Howad et al., 2005), is now available in GDR. CMap displays the prunus bin map with bin names and the first/ last markers of each bin, and the bin-mappded markers are displayed in each bin page. For example, all the bin mapped markers of the first bin in G1 are shown in bin 1:14 page. All the markers in the prunus bin map can be queried through the GDR marker search page. 5. Enhanced SSR server now available with primer generating option. The online SSR server at GDR has been enhanced to include an option to have primers generated for the sequences that users wish to data mine for microsatellites. 6. More databases are available for blast/fasta sequence similarity search. The databases available for blast/fasta sequence similarity search includes the following: peach ESTs, unigenes and ESTs with SSR's, BAC anchored peach ESTs, mapped peach ESTs, almond ESTs and unigenes (Abbott, Clemson U); peach ESTs and unigenes, peach ESTs with SSR's (Vendramin, CRA ISF); octoploid strawberry ESTs, unigenes, and ESTs with SSRs (Folta, U of Florida); diploid strawberry ESTs and unigenes (Davis, U of New Hampshire); ESTs of Fragaria, Malus, Prunus, Pyrus, Rosa, and entire Rosaceae family from NCBI dbEST; NCBI Rosaceae genomic sequences; NCBI Rosaceae protein sequences; Arabidopsis protein sequences from TAIR. A detailed description of the databases is available in each search engine. The blast/fasta sequence servers return the output of the searches in both parsed excel file and as a raw output file with visual alignments. 7. Data available for the three peach BACs that are completely sequenced. Anchored ESTs/markers and the sequences for the three BACs (082I18, 028F08 and pPn31C7) can be accessed from BAC search site. An online annotation pipeline is currently under development by the GDR team. 8. New Rosaceae Executive Committee web page created to provide a communication portal for information and reports generated by the committee. 9. The GDR publications database now contains 242 papers relevant to Rosaceae genetics/genomics. New publications since our last newsletter are listed below: 1. Lazzari B et al. ESTree db: a tool for peach functional genomics. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S16. 2. Patocchi A, Walser M, Tartarini S, Broggini GA, Gennari F, Sansavini S, Gessler C Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm. Genome 2005 Aug;48(4):630-6. 3. Oosumi T, Gruszewski HA, Blischak LA, Baxter AJ, Wadl PA, Shuman JL, Veilleux RE, Shulaev V High-efficiency transformation of the diploid strawberry (Fragaria vesca) for functional genomics. Planta. 2005 Dec 1;:1-12. 4. Gillen, A.M., Bliss, F.A. Identification and Mapping of Markers Linked to the Mi Gene for Root-knot Nematode Resistance in Peach J. Amer. Soc. Hort. Sci. 130(1):24-33. 5. Tzanetakis IE, Martin RR New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus. Virus Res 2005 Sep;112(1-2):32-7. 6. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S, Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG, Motto M, Quarta R Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)]xP. ferganensis BC(1)linkage map: saturation and coverage improvement. Theor Appl Genet 2005 Aug 9;:1-9. 7. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arus P Mapping with a Few Plants: Using Selective Mapping for Microsatellite Saturation of the Prunus Reference Map. Genetics 2005 Aug 22;. 8. Holland D, Larkov O, Bar-Ya'akov I, Bar E, Zax A, Brandeis E, Ravid U, Lewinsohn E Developmental and varietal differences in volatile ester formation and acetyl-CoA: alcohol acetyl transferase activities in apple (Malus domestica Borkh.) fruit. J Agric Food Chem 2005 Sep 7;53(18):7198-203. 9. Gao ZS, Weg WE, Schaart JG, Arkel GV, Breiteneder H, Hoffmann-Sommergruber K, Gilissen LJ Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin). Theor Appl Genet 2005 Sep 6;:1-11. 10. Mohapatra A, Rout GR Identification and analysis of genetic variation among rose cultivars using random amplified polymorphic DNA. Z Naturforsch [C] 2005 Jul-Aug;60(7-8):611-7. 11. Lalli DA, Decroocq V, Blenda AV, Schurdi-Levraud V, Garay L, Le Gall O, Damsteegt V, Reighard GL, Abbott AG Identification and mapping of resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus. Theor Appl Genet 2005 Sep 30;:1-10. 12. Mehli L, Kjellsen TD, Dewey FM, Hietala AM A case study from the interaction of strawberry and Botrytis cinerea highlights the benefits of comonitoring both partners at genomic and mRNA level. New Phytol 2005 Nov;168(2):465-74. 13. Lin C, Mueller LA, Carthy JM, Crouzillat D, Petiard V, Tanksley SD Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 2005 Nov 5;:1-17. 14. Xie H, Sui Y, Chang FQ, Xu Y, Ma RC SSR allelic variation in almond (Prunus dulcis Mill.). Theor Appl Genet 2005 Nov 24;:1-7. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml Work in progress Online EST sequence processing pipeline Annotating peach, plum and apricot BACs. Annotating the rosaceae unigene. Developing a rosaceae BAC annotation pipeline Extending the gene and QTL data available in CMap Integrating data from the USDA CSREES NRI projects

20 years, 1 month

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3rd International Rosaceae Genomics Conference - REMINDERS

by Neill & Sue Page

Goodday everyone Please note the following deadlines: REGISTRATION - early bird closes on 31 December 2005, New Zealand time. To take advantage of the early bird rate you can register online www.rgc3.co.nz and click on the registration tab where you will find all the options available. If you register online then please ensure you complete both sections. ABSTRACTS - for those who have submitted abstract titles and have not yet submitted their abstract these are due by 31 December 2005, New Zealand time. The instructions on the submission of abstracts and format requirements are also available on http://www.rgc3.co.nz Please do not forget to select the most appropriate topic area and include with the abstract. We have received a good number of very interesting titles and are looking forward to the meeting. Best wishes for a Very Merry Christmas and a Great 2006. Regards Sue Page Encore Events Management Ltd 13a Charles St, Westshore Napier, New Zealand Ph/Fax (06) 835 9549 Mobile (027) 669 1345 Email encore.events(a)clear.net.nz

20 years, 2 months

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3rd International Rosaceae Genomics Conference - Abstract Titles

by Neill & Sue Page

Dear All Thank you to those who have already submitted Abstract Titles for the above conference. However, we wish to remind all those who haven't submitted anything yet that the FINAL DAY FOR SUBMISSION IS 31 OCTOBER 2005. If you have any queries please refer to www.rgc3.co.nz, or contact me direct. We look forward to receiving your Abstract Titles. Regards Sue Page Conference Manager Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: (06)835 9549 Mobile: 027 669 1345 Email: encore.events(a)clear.net.nz

20 years, 3 months

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3rd International Rosaceae Genomics Conference - Pre-Conference Workshop

by Neill & Sue Page

Hello everyone, In addition to the RGC3 conference in Napier, a pre-conference workshop will be held in Auckland, 13-17 March 2006. The call for application this workshop was originally 15 October 2005 but is now being extended to 15 November 2005. Please pass the information to any graduate student / young researcher / colleague who may be interested in attending this workshop. A description of the workshop is available on the RCG3 website, www.rgc3.co.nz. Best regards David Chagne Pre-conference Workshop organiser

20 years, 4 months

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3rd International Rosaceae Genomics Conference - March 2006

by Neill & Sue Page

Hello everyone We are pleased to announce that the registration information is now available on our website http://www.rgc3.co.nz Please pass this information on to any colleagues who may be interested in attending this conference. Please read all the information carefully before commencing the registration process. To register online - you will need to complete the online registration form, submit this, then you will be taken to a secure site to process the payment for the registration fee and any activities you select. Alternatively you can download the registration form from the Registration Page and either send in by mail or fax through. If you have any queries please do not hesitate to contact us. REMINDER - that abstract titles are due in by 31 October 2005. As you will see from the website the programme and activites are exciting and we are looking forward to an excellent conference and meeting you there. Regards Sue Page Conference Organiser Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: + 64 (06)835 9549 Mobile: + 64 027 669 1345 Email: encore.events(a)clear.net.nz

20 years, 4 months

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GDR newsletter August 2005

by Sook Jung

GDR Newsletter August 2005 Welcome to the third issue of the GDR newsletter. This newsletter is issued quarterly to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter0705.shtml Attached is the pdf version of this newsletter. What's new at GDR? 1. GDR web address change 2. Updates to peach transcriptome map 3. Anchored genes and ESTs are displayed in genetic maps in CMap 4. New EST data 5. Run InterProScan directly from the EST detail page 6. Bulk search and download feature available in the EST search pages. 7. Abstracts and powerpoint presentations of NRI funded projects available Community News 1. International Symposium on Biotechnology of Temperate Fruit Crops and Tropical Species, Daytona Beach, FL USA, October 10-14, 2005 2. Fruit and Nut Workshop, Saturday January 14, 8 am-12 pm. Plant and Animal Genome Conference XIV, San Diego, January 14-18, 2006. Conference organizer, Dr Amy Iezzoni. 3. 3rd International Rosaceae Genomics Conference in Napier, New Zealand, March 19-23, 2006 What's new at GDR? 1. GDR web address change. GDR is now accessible at the following URL: http://www.rosaceae.org. At the current time this URL will be redirected to http://www.mainlab.clemson.edu/gdr while we move the database over to the new web address. In all future web references to GDR please use the http://www.rosaceae.org URL. 2. Updates to peach transcriptome map. Unique peach ESTs are being hybridized to peach BACs to map the ESTs onto the genetically anchored peach physical map. 569 peach unigenes are anchored to various Rosaceae genetic maps. 367 of them are anchored by direct hybridization to genetically anchored BACs and the rest (202) are anchored by hybridization to BACs that belong to genetically anchored BAC contigs. 375 unigenes are anchored to the TxE map. GDR map viewer and the downloadable peach transcriptome data reflects the updated peach transcriptome map. 3. Anchored genes and ESTs are displayed in genetic maps in CMap. The 25 major genes affecting agronomic characters, anchored to TxE map (Dirlewanger et al, 2004), are now displayed in TxE map in CMap.The peach ESTs are also displayed by the markers with which they share BACs or BAC contigs in hybridization in eight Prunus genetic maps. The anchored ESTs and markers in CMap are linked to GDR detail pages. View an example CMap page. 4. New EST data A new peach EST dataset sequenced by Elisa Vendramin from the CRA Istituto Sperimentale per la Frutticoltura is now publicly available. A total of 1667 clones from peach fruit mesocarp have been analyzed. Assembly of these ESTs produced 1116 putative peach unigenes within this dataset. 5. Run protein motif and domain searches using InterProScan. Users can now search ESTs against the European Bioinformatics Institutes InterPro database directly from GDR. InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to translated ESTs. Finding functional domains in a EST may corroborate the putative function obtained by sequence homology or provide more information for ESTs with no homology to other known proteins. Our site programmatically accesses EBI's InterProScan so users can query InterPro without uploading EST sequences at the EBI's site. To access an example EST page, go to (http://www.mainlab.clemson.edu/java/gdr/EST.jsp? CloneName_Result=PP_LEa0002H11f) and run InterProScan. 6. Bulk search and download feature available in the EST search pages. A bulk search is available for peach, almond, strawberry, and GenBank rosaceae EST datasets. Users can upload a file with multiple clone names or Genbank accession numbers and have returned to them all the sequence and homology information associated with those sequences. Any bulk EST search query will now return downloadable files of fasta formatted sequence and homology results. 7. Abstracts and powerpoint presentations of NRI funded projects. View and download all the abstracts and powerpoint presentations of the NRI funded projects presented at the recent ASHS meeting. Many thanks to the authors and Dr Ed Kaleiko for providing us with this information. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml Work in progress Processing new peach shoot ESTs, rose ESTs from vegetative apices and apices at floral transition and blackberry ESTs Extending the gene and QTL data available in CMap. Integrating data from the USDA CSREES NRI projects Developing a rosaceae EST unigene v2 with enhanced annotation

20 years, 5 months

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3rd International Rosaceae Genomics Conference

by Neill & Sue Page

Dear All We wish to advise that the website for the above conference, www.rgc3.co.nz, has now been updated to include the latest programme and Call for Papers. Please visit the site and complete the pre-registration form if you have not already done so. We will keep you informed as new information is loaded onto the website. If you have any queries please do not hesitate to contact me. Regards Sue Page Conference Organiser Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: (06)835 9549 Mobile: 027 669 1345 Email: encore.events(a)clear.net.nz

20 years, 7 months

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GDR newsletter April 2005

by Sook Jung

GDR Newsletter April 2005 Welcome to the second issue of the GDR newsletter. This newsletter is issued quarterly to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.mainlab.clemson.edu/gdr/newsletter0405.shtml Attached is the pdf version of this newsletter. Community News 1. View the projects funded through the 2004 USDA CSREES National Research Initiative. 2. Announcing 3rd International Rosaceae Genomics Conference in Napier, New Zealand, March 19-23, 2006 3. Rosaceae workshop to be held at the ASHS Annual Meeting in Las Vegas, NV, July 18-21, 2005 4. Download the notes from the 2005 Fruit and Nut Workshop at the Plant and Animal Genome Conference What's new at GDR? 1. Updates to peach physical map 2. Updates to CMap 3. Updates to Genbank Rosaceae EST data 4. Advanced EST search page available 5. Download/view transcriptome data 6. New feature in EST data page 7. Community page available 8. New online analysis tool, SSR server, is available 9. GDR Message Board available 10. GDR web address is changed 1. Updates to the peach physical map The latest peach physical map contains 16895 BACs 1388 contigs. A total of 152 contigs are anchored to the TxE map, the Prunus reference map. The current physical map data was generated from an FPC assembly done on January 6, 2004. WebFPC/WebChrom displays the peach physical map. 2. Updates to CMap 19 Rosaceae genetic maps are available through CMap, the comparative map viewer. Recent addition includes seven apple maps and two cherry maps archived from RoseDB by Anjela Baldo at USDA, ARS PGRU and peach PMP2 map. 3. Updates to GenBank Rosaceae EST data GenBank Rosaceae EST data have been annotated by sequence homology analyses against SwissProt database in addition to GenBank nr protein database. 4. Advanced EST search page available A new comprehensive EST search page is available for the EST datasets. Users can search ESTs in any combination of clone name, organism (genus, species), tissue type, putative function or species of the homologs, and anchored map position where relevant. The search results site has an option for downloading the sequences in fasta format. 5. Download/view transcriptome data The peach transcriptome page provides the current status of the peach transcriptome map and links to an Excel spreadsheet with transcriptome map data detail and other relevant resources. 6. New feature in EST data page A new option, "Printable Data" is available in the EST data page to present all the EST data in one page. View an example page. 7. Community page available Visit our community page for conference news, information on our outreach program and other community resources such as a list of the thirteen projects funded through the 2004 USDA CSREES National Research Initiative: Plant Genome, Bioinformatics, and Genetic Resources. 8. New online analysis tool, SSR server, is available GDR has implemented a new analysis tool, the SSR server. Using this online tool users can upload a batch file of sequences and have summary, individual and fasta formatted library file of the SSR containing sequences returned. The SSR server joins the growing list of online GDR tools such as the CAP3 assembly, FASTA and BLAST servers. 9. Searchable archives of GDR Message Board available Users can view the searchable archives from the gdr mailing list. If you are a registered gdr user you can use the GDR email mailing list gdr-list(a)genome.clemson.edu to send out community based information or requests from your own computer. These emails will automatically be archived onto the message board where they can be searched by subject, thread, author or date. 10. GDR web address is changed. GDR web address is now http://www.mainlab.clemson.edu/gdr/. The old address will be automatically redirected to the new address. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.genome.clemson.edu/gdr/MailingList.shtml Work in progress 1. Processing new peach shoot ESTs and rose ESTs from vegetative apices and apices at floral transition 2. EST search by uploading a list of clone names/accession numbers 3. EST search results site with bulk download feature: Excel files with sequence homology data for the EST search result sets can be downloaded. 4. Development of an online sequence processing tool where users can upload their sequence files (trace or seq and qual files) and have the high quality sequences returned. These in turn can be assembled using the existing CAP3 assembly tool, mined for SSRs using the SSR server and then searched against known plant proteins or rosaceae ESTs using the FASTA and BLAST servers. 5. Tutorials for search and analysis tools 6. Addition of more mapping data.

20 years, 9 months

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3rd International Rosaceae Geonomis Conference

by Neill & Sue Page

Dear All Please find attached the First Announcement for the 3rd International Rosaceae Geonomics Conference which is being held in Napier, New Zealand 19-22 March 2006. Please feel free to forward/distribute this announcement to anyone that you feel may be interested in attending this conference. The website www.rgc3.co.nz is operational and you can complete the pre-registration form online or print out the attached and fax back or send by mail. If you have any queries please do not hesitate to contact me. Regards Sue Page Conference Organiser Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: (06)835 9549 Mobile: 027 669 1345 Email: encore.events(a)clear.net.nz

20 years, 10 months

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Mailing List Name Change

by Stephen Ficklin

The global mailing list for GDR research collaboration has changed names. It is now: GDR-LIST(a)genome.clemson.edu The GDR mailing list currently consists of over 160 email addresses of researchers from all over the world involved with the development of the Genomic Database for Rosaceae. Anyone who is a member of the GDR mailing list may post messages to the group by sending emails to: GDR-LIST(a)genome.clemson.edu If you wish to unsubscribe please visit our web site here: http://www.genome.clemson.edu/gdr/MailingList.shtml Regards, Stephen Ficklin -- Systems Programmer Clemson University Genomics Institute 300 BRC, Clemson University (864) 656-4643 http://www.genome.clemson.edu/

21 years

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GDR newsletter January 2005

by Sook Jung

Welcome to the first issue of the GDR newsletter. This newsletter will be issued quarterly to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form. The online version can be found at http://www.genome.clemson.edu/gdr/newsletter.shtml. Attached is the pdf version of this newsletter. Whats new at GDR? 1. Updates to peach physical map 2. Updates to peach transcriptome map 3. CMap, the comparative map viewer, now available 4. Updates to Rosaceae genetic map data 5. Strawberry EST data are added to GDR 6. Genbank Rosaceae and genera EST assemblies available 7. Data Overview pages are available 8. New Publication search tool is available 9. Navigation bar modified 10. New analysis tool, CAP3 Assembly Server, is available 11. GDR Tutorial is available 12. Fruit Tree Genomics Workshop summary document available 13. GDR published in BMC Bioinformatics 14. GDR presentation at PAG-XIII 15. Enhanced computational resources 1. Updates to the peach physical map The Peach physical map now contains 1223 contigs and 16879 BACs. 134 contigs are anchored to TxE, the Prunus reference map. The current physical map data was generated from an FPC assembly done on October 13, 2004. The next updated version of the physical map will be available at the end of January, 2005. WebFPC/WebChrom displays the peach physical map. 2. Updates to the peach transcriptome map Unique peach ESTs are being hybridized to peach BACs to map the ESTs onto the genetically anchored peach physical map. 294 peach unigenes are anchored to various Rosaceae genetic maps by direct hybridization to genetically anchored BACs. 163 unigenes are anchored to the TxE map. An additional 277 peach unigenes are anchored to genetic maps by hybridization to BACs that belong to genetically anchored BAC contigs. The GDR map viewer displays the updated TxE map with the associated transcriptome map. 3. CMap, the comparative map viewer, now available CMap, a web-based tool that allows users to view comparisons of maps from various species, is implemented at GDR. In this release, we present nine Rosaceae genetic maps. Thanks to all the authors who assisted GDR team for uploading their mapping data. 4. Updates to Rosaceae genetic map data Nine Rosaceae genetic maps are available through CMap, the comparative map viewer. A total of 872 genetic markers from 11 Rosaceae genetic maps are available from the marker search page. 5. Strawberry EST data processed through GDR Over 1800 high quality ESTs from octoploid strawberries (Fragaria x. ananassa) have been annotated and added to GDR. The annotation includes sequence assembly, homology search and SSR mining. Detailed description of the project, sequences, and the annotation results can be searched, browsed and downloaded from the data overview page and EST search site. Thanks to Dr. Kevin Folta at University of Florida for submitting his sequences for processing through the GDR. If you would like to have your sequences processed through the GDR pipeline please contact dorrie(a)genome.clemson.edu. 6. Genbank Rosaceae and genera EST assemblies available All the publicly available Rosaceae ESTs have been assembled using CAP3. Assemblies were also generated for the EST sets of each genus - Malus, Prunus, Fragaria, Rosa and Pyrus. The contigs and singlets for each assembly have bee searched against the Swissprot database and the homology results are available to browse and download in the data overview page. Homology with the NCBI nr protein database and other rosaceae ESTs will be available soon. 7. Data Overview pages are available Data Overview pages are available. For EST projects, users can browse and download the detailed project description and the annotated sequence data. 8. New Publication search tool is available GDR introduces a publication search tool where users can perform Boolean searches by title, author, keyword and publication year. The GDR stores publications from Pubmed that satisfy the following Boolean expression: (Rosaceae OR Prunus OR Rosa OR Fragaria OR Pyrus OR Malus) AND (gene OR genome OR map OR ssr OR microsatellite OR annotation OR est OR marker OR sequence). Relevant publications from sources other than Pubmed may be included. 9. Navigation bar modified GDR has implemented a new navigation bar on top of each page to allow organized and quick access to major features of GDR. Major headings include about us, map resources, search, tools and Rosaceae resources. Each heading has a dropdown menu for a quick access to various pages. 10. New analysis tool, CAP3 Assembly Server, is available GDR has implemented a new analysis tool, the CAP3 assembly server, in addition to the FASTA and BLAST servers. GDR also has links to various useful remote analysis tools. 11. GDR Tutorial is available GDR overview and mapping resources tutorials are now available. Tutorials for search tools and analysis tools will be available soon. 12. Fruit Tree Genomics Workshop summary document available Download the summary report from the October 2004 Technology Roadmap Temperate Fruit Genomics, Genetics and Breeding Workshop at Baltimore, Maryland. 13. GDR published in BMC Bioinformatics GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics. 2004; 5: 130 (Abstract|PDF) 14. GDR presentation at PAG-XIII GDR poster presentation at PAG-XIII, January 15-19, 2005. P830: Genome Database For Rosaceae (GDR) 15. Enhanced Computational Resources In January 2005, Clemson University purchases a 32 node apple grid to enhance the computational infrastructure of the CUGI Bioinformatics Center. This equipment will help ensure that data analysis in GDR remains current and readily available to the Rosaceae community. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.genome.clemson.edu/gdr/MailingList.shtml Work in progress 1. Processing new peach shoot ESTs and rose ESTs from vegetative apices and apices at floral transition 2. New comprehensive EST search site: Search by putative function from tissue, sequence homology and anchored map position will be available in addition to current search categories. 3. EST search results site with bulk download feature: Sequences in Fasta format and homology results for the EST search result sets can be downloaded. 4. Tutorials for search and analysis tools.

21 years, 1 month

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