GDR-LIST

gdr-list@bioinfo.wsu.edu

1 participants
329 discussions

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, 2 months

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, 2 months

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, 2 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 >

18 years, 3 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

18 years, 3 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

18 years, 3 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

18 years, 3 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.

18 years, 3 months

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, 4 months

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, 4 months

← Newer
1
...
26
27
28
29
30
31
32
33
Older →

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

GDR-LIST