GDR-LIST July 2007

gdr-list@bioinfo.wsu.edu

4 participants
6 discussions

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

16 years, 9 months

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 >

16 years, 9 months

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

16 years, 9 months

[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

16 years, 9 months

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

16 years, 9 months

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.

16 years, 9 months

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GDR-LIST July 2007