- GDR-LIST - Main Bioinformatics Lab

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

18 years, 11 months

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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

18 years, 11 months

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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

18 years, 11 months

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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

18 years, 11 months

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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.

18 years, 11 months

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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

18 years, 11 months

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test

by Svancara Randall

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

19 years

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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

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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

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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, 1 month

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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, 1 month

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by MARIAJO RUBIO

19 years, 2 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, 3 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, 3 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, 3 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, 6 months

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(no subject)

by Yanmin Zhu

19 years, 8 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, 9 months

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

by Angela M. Baldo

19 years, 10 months

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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

19 years, 10 months

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GDR Newsletter January 2006 pdf attachment

by Sook Jung

19 years, 11 months

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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

19 years, 11 months

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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

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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, 1 month

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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, 2 months

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