- GDR-LIST - Main Bioinformatics Lab

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, 2 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, 3 months

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Zaragoza

by riccardo.velasco＠iasma.it

18 years, 3 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, 3 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, 3 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, 3 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, 3 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, 3 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, 3 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, 4 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, 4 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, 4 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, 4 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, 5 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, 5 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, 5 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, 6 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, 6 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, 6 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, 7 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, 7 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, 7 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, 9 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

18 years, 10 months

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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 ---------------------------------------------------------------------

18 years, 11 months

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