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).
---------------------------------------------------------------------
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.
___________________________________________________________________
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
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
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
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
<<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
>
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
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
> 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
