Dear RosCAP coordinators/advisors and RosEXEC members,
See messages below. Some of you will be getting this for the fifth time, but others for the first time, and the latter is the reason for this wide email list. You represent RosCAP proposal PIs, RosCAP proposal advisory boards, and RosEXEC members, with some redundancies.
Call-in details for the teleconference scheduled for today (Monday) at 3:30pm EDT are at the bottom of the email. Your participation is important.
Cameron
________________________________
From: Amy F Iezzoni [mailto:iezzoni@msu.edu] Sent: Sun 6/29/2008 7:26 PM To: aalbert@CLEMSON.EDU Cc: amdandekar@ucdavis.edu; chris.dardick@ars.usda.gov; Peace, Cameron; ebenezer@uckac.edu; eric.vandeweg@wur.nl; GF35@cornell.edu; hancock@msu.edu; hsa1@cornell.edu; hsilva@unab.cl; Korban@uiuc.edu; mcferson@treefruitresearch.com; Michael.Wisniewski@ars.usda.gov; Pere.Arus@irta.cat; riccardo.velasco@iasma.it; sgardiner@hortresearch.co.nz; skb3@cornell.edu; tom.davis@unh.edu Subject: Re: RosCAP
Hello everyone,
First of all, thanks Bert for checking with Ed. Disappointing, but at least we know what our opportunities are. Clearly we need to put together a proposal that addresses our most critical needs. Although we have not seen the call for proposals, I understand that there has been some discussion of what the community might wish to put forward within the RosEXEC discussions that Gennaro has been convening. Cameron filled me in on the developing concept as I am not on RosEXEC.
Basically, I felt that the outline that Cameron and Gennaro et al. were discussing is really compelling. It addresses two critical needs: the need for Pedigree Based Analysis (formally called pedigree genotyping) for rosaceous breeders, and eliminating the disconnect between QTL discovery and marker assisted selection. Also importantly it keeps the items that were reviewed positively in the proposal (Pedigree based analysis and a willingness to address multiple traits), yet eliminates what was criticized, QTL discovery with genome scans relying on existing markers. The focus, would be QTL validation and allele mining based upon already reported QTLs (e.g. QTL for acidity, QTL for bloom date, gene for self fertility etc)and ending with the application of MAS. This eliminates the need for the genome scans, thereby making the project more "downstream" with a direct impact for cultivar development. With this scenario, matching funds could relatively easily come from the breeding programs themselves, with their associated industries and other support, and partial salaries of participating RosCAP personnel.
Cameron outlined the items for me as follows:
1. Robustness of marker-trait associations over germplasm (validating that an association identified in, for example, a specific experimental population is valid across a wider range of germplasm). 2. Specific applicability of marker-trait associations to breeding programs (validate associations in breeder's own germplasm, determine QTL alleles present in each potential parent), where appropriate (i.e. where the trait is actually of priority in the breeding program). 3. Enable marker-assisted selection for each breeding program (high-throughput capacity - identify local source or develop center, determine best stage to implement genotyping according to idiosyncrasies of operations). 4. Demonstrate implementation of MAS in each breeding program (e.g. use appropriate markers on several thousand seedlings). 5. Routine application in breeding programs (this is the deliverable).
Successful completion of items 1 and 2 above relies on the use of Pedigree Based Analysis, as it is an excellent tool for QTL validation and allele mining. Apparently Cameron and Gennaro were discussing combining this with a common Rosaceae breeder's database (develop our own, or use AppleBreed, or both)hosted on the GDR, and interoperable with other database efforts such as GDR itself, GRIN Global, Rosaceae Standardized Phenotyping, etc. and.. even a Rosaceae Genomics, Genetics, and Breeding Forum (from an idea discussed in a previous 2008 RosEXEC teleconference - an online forum for publishing short articles, peer-reviewed by community).
Anyway, a lot to think about, and thank you to those of you on RosEXEC that have been kicking this around. My only suggestion is that we probably need a wider email audience for continuing discussions. I don't have a wider list at home, but if any of you have the RosEXEC mailing list or RosCAP PI lists, those lists would be appropriate to include.
I look forward to our discussion tomorrow.
Best wishes, Amy
aalbert@CLEMSON.EDU writes:
Folks, I have received Ed's response to my query about the future of RosCAP, I have copied it below. It appears that the SCRI is our chance now and that we will not be competitive in the future plant genome program. I am therefore going to resubmit it after revision. I would like to know who is interested in participating and can provide a match for their portion. I can cut this in various ways if needed so I need to know who is in before I can proceed. Please respond asap on this. Chris or Cameron, can you forward this information to the complete CAP group as I only have the core group e-mail list. Bert
Ed's response:
Bert,
Given that SCRI now exists, RosCAP would probably not be as competitive in the NRI CAP program. The reorganization of CSREES to NIFA and NRI to AFRI may change things a bit as well so take advantage of SCRI as much as possible this year. I would suggest submitting RosCAP to SCRI this year with as many revisions as possible, if not, plan to submit to SCRI next year, not plant genome. If folks have well developed separate initiatives, submit them to SCRI as well to take advantage of an opportunity that fits perfectly with the rosaceae genomics, genetics and breeding, so don't let it slip away. A key to SCRI is the matching funds requirement so talk to Tom Bewick about that.
PARTICIPANT ACCESS INFORMATION:
-------------------------------
PARTICIPANT PASSCODE: 2402523
TO JOIN A CONFERENCE
1) You must use a touch-tone phone to participate in an Instant Meeting
Conference.
2) Dial the appropriate access number
3) Enter numeric passcode followed by a "#"
------------------------------------------------------------------------------
LEADER & PARTICIPANT ACCESS INFORMATION
---------------------------------------
Click http://www.mymeetings.com/audioconferencing/globalAccessFAQ.php https://connect.wsu.edu/exchweb/bin/redir.asp?URL=http://www.mymeetings.com/audioconferencing/globalAccessFAQ.php for information on specific country access dialing.
Country Toll Numbers Freephone/Toll Free Number
ARGENTINA 0800-777-0515
AUSTRALIA ADELAIDE: 61-8-8121-4883 1-800-659-380
AUSTRALIA BRISBANE: 61-7-3102-0985 1-800-659-380
AUSTRALIA CANBERRA: 61-2-6100-1985 1-800-659-380
AUSTRALIA MELBOURNE: 61-3-9010-7754 1-800-659-380
AUSTRALIA PERTH: 61-8-9467-5264 1-800-659-380
AUSTRALIA SYDNEY: 61-2-8205-8123 1-800-659-380
AUSTRIA 43-1-92-81-120 0800-005-266
BELGIUM 32-2-400-9824 0800-3-8744
BRAZIL 0800-8911988
CHILE 1230-020-2638
CHINA* 10800-712-1677
10800-120-1677
COLOMBIA 01800-9-156477
CZECH REPUBLIC 420-2-25-98-56-73 800-700-235
DENMARK 45-7014-0300 8088-8304
FINLAND 358-106-33-205 0-800-9-14607
FRANCE LYON: 33-4-26-69-12-99 080-563-6110
FRANCE MARSEILLE: 33-4-86-06-00-99 080-563-6110
FRANCE PARIS: 33-1-76-74-24-94 080-563-6110
GERMANY 49-69-2222-4873 0800-664-4254
GREECE 30-80-1-100-0698 00800-12-7310
HONG KONG 852-2286-5729 800-933-921
HUNGARY 06-800-13830
INDIA 000-800-852-1264
INDONESIA 001-803-011-3973
IRELAND 353-1-247-5678 1800-992-935
ISRAEL 1-80-9216159
ITALY 39-02-3600-6016 800-986-993
JAPAN OSAKA: 81-6-7739-4783 0044-22-132424
JAPAN TOKYO: 81-3-5539-5187 0044-22-132424
LUXEMBOURG 352-27-000-1384
MALAYSIA 1-800-81-3069
MEXICO 001-866-295-6360
NETHERLANDS 31-20-718-8596 0800-023-1812
NEW ZEALAND 64-9-970-4767 0800-450-789
NORWAY 47-21-590-072 800-15308
PANAMA 011-001-800-5072111
POLAND 00-800-1212569
PORTUGAL 8008-14054
RUSSIA 8-10-8002-0114011
SINGAPORE 65-6883-9226 800-120-4675
SLOVAK REPUBLIC 421-2-322-422-39
SOUTH AFRICA 080-09-80424
SOUTH KOREA 82-2-6744-1079 00798-14800-7189
SPAIN 34-91-414-25-40 800-300-060
SWEDEN 46-8-566-19-397 0200-884-614
SWITZERLAND 41-44-580-6402 0800-120-039
TAIWAN 886-2-2795-7375 00801-137-796
THAILAND 001-800-1206-66050
UNITED KINGDOM BIRMINGHAM: 44-121-210-9039 0808-238-6019
UNITED KINGDOM GLASGOW: 44-141-202-3239 0808-238-6019
UNITED KINGDOM LEEDS: 44-113-301-2139 0808-238-6019
UNITED KINGDOM LONDON: 44-20-3043-2499 0808-238-6019
UNITED KINGDOM MANCHESTER: 44-161-601-1439 0808-238-6019
URUGUAY 000-413-598-3460
USA 1-517-466-2232 866-692-3582
VENEZUELA 0800-1-00-3782
I just had something come up and I may not be able to make the call. Below is my input just in case I can't make it.
Thanks Amy for the nice summary of Cameron and Gennaro's ideas and pointing out the problems with our various e-mail lists. I think if we use both the RosEXEC and RosCAP PI lists we should cover everyone from now on. Perhaps separate conference calls will be needed for the RosCAP Research, Education, Extension committees to address each component.
I agree that Cameron and Gennaro are on target and address many of the reviewers concerns about the research plan. I also agree with Eric that we should not just "patch" what we have written. Since it may help the discussion later today, I tried to organize the various reviewer comments in a way that should help our ongoing discussions. I did not include everything, only things I thought might be more difficult to address.
Negative aspects: 1) GENERAL ISSUES: "The proposal gives far few details" "the organization and structure of the proposal, in particular the degree of parsing the components, made review of the proposal difficult.""presents no clear timeline to reach the desired milestones" 2) INTEGRATION: "..this synergy is not apparent. Little coordination exists among the different research groups." "no integration of how talents are applied in a synergistic manner". 3) IMPACT ON BREEDING: "The current shortfall of plant breeders is unclear as is how much [we] will impact that shortfall" "It is unclear how many breeders will be impacted by this effort" "How many breeders are in the Rosaceae community and how many currently use MAB" "the approaches to address this problem [shortfall of breeders] are not clearly distinct from current (and mostly unsuccessful programs)" 4) RESEARCH PLAN: "the proposal conflates QTL mapping with MAS." "It is unclear what breeder's toolkits are exactly" "Do the PIs expect that the recombination present within their pedigrees is sufficient to identify markers very closely linked to the QTL?" "actual translation to breeding never seems to show up [in the proposal]." "I am struck by the fact that...there is very little discussion on the development of markers""no underlying theory for any of the traits, but rather a request for a fishing expedition" 5) EXTENSION: "the extension proposed to growers and extension specialists is traditional" "Assessment of education/extension outcomes is not described" "who will develop the specialty workshops and what is their expertise" "Integration of extension service into academic programs...should be an institutional goal" "It is unclear how stakeholders benefit from extension efforts" "role of extension coordinator not clearly defined" "there is no clear plan for sustained education or extension beyond the life of the project" "neither education or extension teams list an industry partner" 6) EDUCATION: "the methods and approach are high risk" "are students being educated to enter careers in plant breeding or into graduate careers to be researchers"--This is exactly the kind of attitude we need to change."[student] recruitment is not well defined" "the graduate training does not seem to go beyond the normal training of students in the applicant's laboratory" "no letters of support from Universities that curriculum changes are welcome" ""[proposed] coursework is not distinct from standard curricula and it is unclear why such courses...need to be developed""there is no evidence of this CAP leveraging the efforts and success of other CAPS" 7) BUDGET "no clear plan for the distribution of the "Future National Interest" money." "it is very hard to determine the distribution of funds among the 3 priorities" "can not find money for workshops or strategic planning sessions"
Positive aspects:
1) RELEVANCE: "The fruit crops are of great economic value and could benefit from enhanced academic programs"
2) INTEGRATION: "The group has strenghts in breeding, specifically molecular breeding""The team integration proposed would establish professional relationships and understanding that are key to modern plant breeding"
3) RESEARCH PLAN: "QTL discovery in breeding populations is very desirable...and use of FlexQTL is a strength."
4) EXTENSION: "something that is of interest, however, are programs discussing plant breeding in general... This is something farmers and others are interested in."
5) EDUCATION: "identified the correct target population for...educating the next generation of plant breeders""Facilitating a mentoring role for graduate students was an excellent decision, as was early stakeholder involvment""one distinction [of our education plan] is exposure to 'breeders, growers, industry representatives and research scientists', but this piece needs to be emphasized" "the plan for sub-group teams for the students to join is attractive..." "the idea of developing a cohort of students from different universities....is really good." "using an original way...allowing students to continue in their chosen undergraduate field of interest but train them in modern breeding methodologies."
Chris Dardick USDA, ARS Appalachian Fruit Research Station 2217 Wiltshire Road Kearneysville, WV 25430 phone: 304-725-3451 ext. 387 fax: 304-728-2340 chris.dardick@ars.usda.gov
________________________________
From: Peace, Cameron [mailto:cpeace@wsu.edu] Sent: Monday, June 30, 2008 9:58 AM To: aalbert@clemson.edu; Dardick, Chris; iezzoni@msu.edu; Korban@uiuc.edu; tom.davis@unh.edu; nbassil@ars-grin.gov; hancock@msu.edu; amdandekar@ucdavis.edu; Olmstead, James Winston; eric.vandeweg@wur.nl; gf35@cornell.edu; Main, Doreen; bryon_sosinski@ncsu.edu; skb3@cornell.edu; pere.arus@irta.es; sbrft@clemson.edu; SGardiner@hortresearch.co.nz; david.harry@oregonstate.edu; lemauxpg@nature.berkeley.edu; dbneale@ucdavis.edu; hsilva@unab.cl; smith376@umn.edu; riccardo.velasco@iasma.it; gvansickle@caltreefruit.com; fbliss@dcn.org; Jim McFerson; rcurtis@almondboard.com; chalmers@titanfarms.com; rosexec-list@bioinfo.wsu.edu Subject: RosCAP and SCRI
Dear RosCAP coordinators/advisors and RosEXEC members,
See messages below. Some of you will be getting this for the fifth time, but others for the first time, and the latter is the reason for this wide email list. You represent RosCAP proposal PIs, RosCAP proposal advisory boards, and RosEXEC members, with some redundancies.
Call-in details for the teleconference scheduled for today (Monday) at 3:30pm EDT are at the bottom of the email. Your participation is important.
Cameron
________________________________
From: Amy F Iezzoni [mailto:iezzoni@msu.edu] Sent: Sun 6/29/2008 7:26 PM To: aalbert@CLEMSON.EDU Cc: amdandekar@ucdavis.edu; chris.dardick@ars.usda.gov; Peace, Cameron; ebenezer@uckac.edu; eric.vandeweg@wur.nl; GF35@cornell.edu; hancock@msu.edu; hsa1@cornell.edu; hsilva@unab.cl; Korban@uiuc.edu; mcferson@treefruitresearch.com; Michael.Wisniewski@ars.usda.gov; Pere.Arus@irta.cat; riccardo.velasco@iasma.it; sgardiner@hortresearch.co.nz; skb3@cornell.edu; tom.davis@unh.edu Subject: Re: RosCAP
Hello everyone,
First of all, thanks Bert for checking with Ed. Disappointing, but at least we know what our opportunities are. Clearly we need to put together a proposal that addresses our most critical needs. Although we have not seen the call for proposals, I understand that there has been some discussion of what the community might wish to put forward within the RosEXEC discussions that Gennaro has been convening. Cameron filled me in on the developing concept as I am not on RosEXEC.
Basically, I felt that the outline that Cameron and Gennaro et al. were discussing is really compelling. It addresses two critical needs: the need for Pedigree Based Analysis (formally called pedigree genotyping) for rosaceous breeders, and eliminating the disconnect between QTL discovery and marker assisted selection. Also importantly it keeps the items that were reviewed positively in the proposal (Pedigree based analysis and a willingness to address multiple traits), yet eliminates what was criticized, QTL discovery with genome scans relying on existing markers. The focus, would be QTL validation and allele mining based upon already reported QTLs (e.g. QTL for acidity, QTL for bloom date, gene for self fertility etc)and ending with the application of MAS. This eliminates the need for the genome scans, thereby making the project more "downstream" with a direct impact for cultivar development. With this scenario, matching funds could relatively easily come from the breeding programs themselves, with their associated industries and other support, and partial salaries of participating RosCAP personnel.
Cameron outlined the items for me as follows:
1. Robustness of marker-trait associations over germplasm (validating that an association identified in, for example, a specific experimental population is valid across a wider range of germplasm). 2. Specific applicability of marker-trait associations to breeding programs (validate associations in breeder's own germplasm, determine QTL alleles present in each potential parent), where appropriate (i.e. where the trait is actually of priority in the breeding program). 3. Enable marker-assisted selection for each breeding program (high-throughput capacity - identify local source or develop center, determine best stage to implement genotyping according to idiosyncrasies of operations). 4. Demonstrate implementation of MAS in each breeding program (e.g. use appropriate markers on several thousand seedlings). 5. Routine application in breeding programs (this is the deliverable).
Successful completion of items 1 and 2 above relies on the use of Pedigree Based Analysis, as it is an excellent tool for QTL validation and allele mining. Apparently Cameron and Gennaro were discussing combining this with a common Rosaceae breeder's database (develop our own, or use AppleBreed, or both)hosted on the GDR, and interoperable with other database efforts such as GDR itself, GRIN Global, Rosaceae Standardized Phenotyping, etc. and.. even a Rosaceae Genomics, Genetics, and Breeding Forum (from an idea discussed in a previous 2008 RosEXEC teleconference - an online forum for publishing short articles, peer-reviewed by community).
Anyway, a lot to think about, and thank you to those of you on RosEXEC that have been kicking this around. My only suggestion is that we probably need a wider email audience for continuing discussions. I don't have a wider list at home, but if any of you have the RosEXEC mailing list or RosCAP PI lists, those lists would be appropriate to include.
I look forward to our discussion tomorrow.
Best wishes, Amy
aalbert@CLEMSON.EDU writes:
Folks, I have received Ed's response to my query about the future of RosCAP, I have copied it below. It appears that the SCRI is our chance
now
and that we will not be competitive in the future plant genome
program. I
am therefore going to resubmit it after revision. I would like to
know
who is interested in participating and can provide a match for their portion. I can cut this in various ways if needed so I need to know
who
is in before I can proceed. Please respond asap on this. Chris or Cameron, can you forward this information to the complete CAP group as
I
only have the core group e-mail list. Bert
Ed's response:
Bert,
Given that SCRI now exists, RosCAP would probably not be as
competitive
in the NRI CAP program. The reorganization of CSREES to NIFA and NRI
to
AFRI may change things a bit as well so take advantage of SCRI as much as possible this year. I would suggest submitting RosCAP to SCRI
this
year with as many revisions as possible, if not, plan to submit to
SCRI
next year, not plant genome. If folks have well developed separate initiatives, submit them to SCRI as well to take advantage of an opportunity that fits perfectly with the rosaceae genomics, genetics
and
breeding, so don't let it slip away. A key to SCRI is the matching funds requirement so talk to Tom Bewick about that.
PARTICIPANT ACCESS INFORMATION:
-------------------------------
PARTICIPANT PASSCODE: 2402523
TO JOIN A CONFERENCE
1) You must use a touch-tone phone to participate in an Instant Meeting
Conference.
2) Dial the appropriate access number
3) Enter numeric passcode followed by a "#"
------------------------------------------------------------------------ ------
LEADER & PARTICIPANT ACCESS INFORMATION
---------------------------------------
Click http://www.mymeetings.com/audioconferencing/globalAccessFAQ.php https://connect.wsu.edu/exchweb/bin/redir.asp?URL=http://www.mymeetings .com/audioconferencing/globalAccessFAQ.php for information on specific country access dialing.
Country Toll Numbers Freephone/Toll Free Number
ARGENTINA 0800-777-0515
AUSTRALIA ADELAIDE: 61-8-8121-4883 1-800-659-380
AUSTRALIA BRISBANE: 61-7-3102-0985 1-800-659-380
AUSTRALIA CANBERRA: 61-2-6100-1985 1-800-659-380
AUSTRALIA MELBOURNE: 61-3-9010-7754 1-800-659-380
AUSTRALIA PERTH: 61-8-9467-5264 1-800-659-380
AUSTRALIA SYDNEY: 61-2-8205-8123 1-800-659-380
AUSTRIA 43-1-92-81-120 0800-005-266
BELGIUM 32-2-400-9824 0800-3-8744
BRAZIL 0800-8911988
CHILE 1230-020-2638
CHINA* 10800-712-1677
10800-120-1677
COLOMBIA 01800-9-156477
CZECH REPUBLIC 420-2-25-98-56-73 800-700-235
DENMARK 45-7014-0300 8088-8304
FINLAND 358-106-33-205 0-800-9-14607
FRANCE LYON: 33-4-26-69-12-99 080-563-6110
FRANCE MARSEILLE: 33-4-86-06-00-99 080-563-6110
FRANCE PARIS: 33-1-76-74-24-94 080-563-6110
GERMANY 49-69-2222-4873 0800-664-4254
GREECE 30-80-1-100-0698 00800-12-7310
HONG KONG 852-2286-5729 800-933-921
HUNGARY 06-800-13830
INDIA 000-800-852-1264
INDONESIA 001-803-011-3973
IRELAND 353-1-247-5678 1800-992-935
ISRAEL 1-80-9216159
ITALY 39-02-3600-6016 800-986-993
JAPAN OSAKA: 81-6-7739-4783 0044-22-132424
JAPAN TOKYO: 81-3-5539-5187 0044-22-132424
LUXEMBOURG 352-27-000-1384
MALAYSIA 1-800-81-3069
MEXICO 001-866-295-6360
NETHERLANDS 31-20-718-8596 0800-023-1812
NEW ZEALAND 64-9-970-4767 0800-450-789
NORWAY 47-21-590-072 800-15308
PANAMA 011-001-800-5072111
POLAND 00-800-1212569
PORTUGAL 8008-14054
RUSSIA 8-10-8002-0114011
SINGAPORE 65-6883-9226 800-120-4675
SLOVAK REPUBLIC 421-2-322-422-39
SOUTH AFRICA 080-09-80424
SOUTH KOREA 82-2-6744-1079 00798-14800-7189
SPAIN 34-91-414-25-40 800-300-060
SWEDEN 46-8-566-19-397 0200-884-614
SWITZERLAND 41-44-580-6402 0800-120-039
TAIWAN 886-2-2795-7375 00801-137-796
THAILAND 001-800-1206-66050
UNITED KINGDOM BIRMINGHAM: 44-121-210-9039 0808-238-6019
UNITED KINGDOM GLASGOW: 44-141-202-3239 0808-238-6019
UNITED KINGDOM LEEDS: 44-113-301-2139 0808-238-6019
UNITED KINGDOM LONDON: 44-20-3043-2499 0808-238-6019
UNITED KINGDOM MANCHESTER: 44-161-601-1439 0808-238-6019
URUGUAY 000-413-598-3460
USA 1-517-466-2232 866-692-3582
VENEZUELA 0800-1-00-3782
-
Dardick, Chris -
Peace, Cameron