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(a)ars.usda.gov ________________________________ From: Peace, Cameron [mailto:cpeace@wsu.edu] Sent: Monday, June 30, 2008 9:58 AM To: aalbert(a)clemson.edu; Dardick, Chris; iezzoni(a)msu.edu; Korban(a)uiuc.edu; tom.davis(a)unh.edu; nbassil(a)ars-grin.gov; hancock(a)msu.edu; amdandekar(a)ucdavis.edu; Olmstead, James Winston; eric.vandeweg(a)wur.nl; gf35(a)cornell.edu; Main, Doreen; bryon_sosinski(a)ncsu.edu; skb3(a)cornell.edu; pere.arus(a)irta.es; sbrft(a)clemson.edu; SGardiner(a)hortresearch.co.nz; david.harry(a)oregonstate.edu; lemauxpg(a)nature.berkeley.edu; dbneale(a)ucdavis.edu; hsilva(a)unab.cl; smith376(a)umn.edu; riccardo.velasco(a)iasma.it; gvansickle(a)caltreefruit.com; fbliss(a)dcn.org; Jim McFerson; rcurtis(a)almondboard.com; chalmers(a)titanfarms.com; rosexec-list(a)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(a)CLEMSON.EDU Cc: amdandekar(a)ucdavis.edu; chris.dardick(a)ars.usda.gov; Peace, Cameron; ebenezer(a)uckac.edu; eric.vandeweg(a)wur.nl; GF35(a)cornell.edu; hancock(a)msu.edu; hsa1(a)cornell.edu; hsilva(a)unab.cl; Korban(a)uiuc.edu; mcferson(a)treefruitresearch.com; Michael.Wisniewski(a)ars.usda.gov; Pere.Arus(a)irta.cat; riccardo.velasco(a)iasma.it; sgardiner(a)hortresearch.co.nz; skb3(a)cornell.edu; tom.davis(a)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(a)CLEMSON.EDU writes: now program. 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