________________________________
From: Bert Abbott [mailto:aalbert@CLEMSON.EDU]
Sent: Wednesday, October 17, 2007 11:47 AM
To: Dardick, Chris
Subject: Re: RosCAP website
Chris, here is a pdf. of the CAP portion of the NRI RFA. Please send
it to all so that they can see the emphasis. Also note that the amount
is 5 million for 4 years but that these are envisioned to be
continuation type projects with continued funding. Bert
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
Dr. Amy Iezzoni
Professor
Department of Horticulture
Michigan State University
East Lansing, MI 48824
telephone: (517) 355-5191 ext. 391
fax: (517) 353-0890
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.
___________________________________________________________________
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
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
