NRSP-8: NAGRP Aquaculture Genome Program

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From: John Liu []
Sent: Wed, 21 Dec 2005 16:11:48 -0600
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 7

o  The Aquaculture Genomics Workshop will be held January 14-15, 2006 at 
the Town and Country Hotel in San Diego along with the XIV Plant and 
Animal Genome (PAG XIV) Conference.  The program can be found at Dr. Caird Rexroad is the 
organizer for the Workshop, if you have any questions, please contact 
Dr. Rexroad (  
o  Congratulations to the recipients of the Aquaculture Genomics 
Student/postdoc Travel Award: In order to increase participation of 
graduate students and postdoctoral fellows in Aquaculture Genomics 
Workshop, the Aquaculture group of the NRSP8 has set aside a significant 
proportion of its funding to support the participation of young 
scientists in aquaculture genome research.  This year, the following 12 
individuals has been selected as the winners of the Travel Award by 
Aquaculture Genome Executive Committee:

            Jun-ichi Hikima (Medical University of South Carolina)
            Nuala Oleary (Medical University of South Carolina)
            Raviv Shaul (BGU)
            Valerie Barbosa (INRA)
            Charlene Couch (North Carolina State University)
            Amber Garber (North Carolina State University)
            Avner Cnaani (University of New Hampshire)
            Bo-Young Lee (University of New Hampshire)
            Peng Xu (Auburn University)
            Takashi Koyama (TUMST)
            Yongping Wang (Rutgers University)
            Lingling Wang (Rutgers University)
o  The NRSP8 Business Meeting will be held on January 15, 2006 in 
conjunction with the Plant and Animal Genome XIV Conference in San Diego 
from 4:30 PM to 6:00 PM in the Royal Palm 3 and 4 of the Town and Country 
Hotel.  If you have any questions on this business meeting, please 
contact Dr. Colin Kaltenbach ( You are encouraged 
to participate in the meeting.
o  SEND your USDA-funded success stories to CSREES Muquarrab Qureshi, 
NAGRP Leader, who is revising the CSREES Animal Breeding, Genetics and 
Genomics webpage, He 
requests short features that highlight the impact of your research on 
animal agriculture and wellbeing. Pictures and/or web links, links to key 
publications, journal cover pages, or other stories are welcome.  Please 
indicate if the work was supported by USDA and/or any federal or industry 
partnership. Send your material to Thanks in 
advance for your help.
o  Concerning the USDA NRI Functional Genomics funding, many of you have 
expressed your concerns.  I have communicated with Dr. Anna Palmisano, 
Deputy Administrator of CSREES, and the following is her response in an 
e-mail of November 1, 2005:

Dear Dr. Liu and colleagues,

Thank you for your e-mail addressing the Functional Genomics program 
element of the Animal Genome Program in the National Research Initiative 
(NRI) FY 06 RFA. A similar e-mail was sent to Dr. Burfening, so I'd like 
to take the opportunity to respond on behalf of us both. 

The input from the aquaculture community's white paper was very important 
in the FY06 RFA process.  There is no question that the aquaculture 
community's input and other stakeholder groups resulted in continuation 
of the Tools and Reagents program, which was slated to be terminated in 
FY 06. Note that the Tools and Reagents program has been renamed "Tools and 
Resources" and "Bioinformatics" in the FY 06 RFA.

The FY 06 animal genome program chose to focus the functional genomics 
element on species with sequenced genomes for a number of important 
reasons. As you know, the federal government, taxpayers, and industry 
have made an enormous investment in whole genome sequencing efforts for a 
limited number of agricultural animal species. Species with 5X species 
are well-positioned to move into analysis for functional genomics. 
Functional genomics is the next logical step to relate gene function to 
the vast amount of information that is being derived from the sequencing 
efforts for a limited number of agricultural animal species. Moreover, 
focusing on species for which 5X sequence is available is more likely to 
provide a return on the sequencing investment for the public in a shorter 
time frame. 

It is important to note that other animal-related programs in the NRI 
will accept proposals in the functional genomics area on species that do 
not have a 5X genome sequence, if those proposals relate to the specific 
FY 06 program priorities.

We have also been also very concerned about the low success rates in the 
animal functional genomics program in the past two cycles of funding (12% 
success rate) and the huge investment of scientists' time and effort to 
write proposals with little chance of success.  Additionally, the 
significant time, effort and costs involved in the review of a large 
number of proposals (relative to availability of funds) was another part
of this consideration.

The NRI National Program Leaders and our administrators have been using 
the logic model in the NRI program planning process.  We have been 
developing short-term, mid-term and long-term goals from which 
performance of the research portfolio will be evaluated against. 
Using this model, we are working with the stakeholder community to 
develop a shared vision for the future of NRI programs. We are 
identifying priorities and requesting proposals that will help achieve 
mission relevant goals and quantifiable impacts. 

We are currently beginning the FY 07 NRI RFA planning process; 
prioritized input from stakeholder groups is always welcome and 
important for our RFA planning process. The Animal Functional Genomics 
program element will not be solicited in the FY 07 RFA, but the NRI 
Animal Genome Program will most likely be soliciting for functional 
genomics proposals in the FY 08 RFA.  As we begin planning for the FY 08 
RFA we will again consider potential focus areas for the Animal Genome 
program elements; your input would be very valuable.

Please feel free to contact me if you have any questions. We appreciate 
your interest in the NRI.

Anna Palmisano

Anna C. Palmisano, Ph.D.
Deputy Administrator, Competitive Programs
Cooperative State Research, Education and Extension Service
800 9th St., SW, Waterfront Centre
Washington, D.C. 20024-2241
Phone: 202-401-1761
FAX: 202-401-1782
o  Dr. Thomas D. Kocher has drafted a letter on next page to CSREES of 
USDA concerning NRI Functional Genomics funding for your approval.  If 
you support the letter, please send an e-mail to Dr. Kocher 
( including your name and institutional affiliations.  
USDA has been very receptive of community input as demonstrated by the 
preservation of the Genome Reagents and Tools Program.

December 21, 2005
Dr. Colien Hefferan, Administrator
Cooperative State Research, Education, and Extension Service
United States Department of Agriculture
1400 Independence Avenue SW., Stop 2201
Washington, DC 20250-2201
Dear Dr. Hefferan,
We were surprised and dismayed by the language in the 2006 NRI RFP for 
the Animal Genome: Functional Genomics (43.0D).  Specifically, we object 
to the restriction of the competition to species which have at least 5x 
coverage over 90% of the genome.  This rule puts half of the Animal 
Genome funds out of the reach of investigators working on aquaculture 
Besides being clearly discriminatory against unsequenced species, it 
ignores the fact that excellent functional genomic research is already 
being done with cDNA microarrays.  High quality microarrays are now 
available for a number of aquaculture species (e.g. the GRASP efforts on 
salmonids).  These microarrays are entirely appropriate for gene expression 
More important, this restriction discourages innovation. It stifles the 
development of new and creative approaches to functional genomics.  For 
example, transcript profiling no longer requires a genome sequence or 
extensive cDNA resources.  With inexpensive sequencing technologies from 
454 Life Science or Solexa it is now possible to perform in-depth 
expression profiling of new species at relatively low cost.  And there 
are many other approaches to functional genomics besides transcriptional 
The restrictive language in the RFP is in any case inappropriate because 
all proposals should be evaluated on their individual merits.  Proposals 
to work on species with relatively complete genome sequences will 
naturally have a leg up in the competition. But why exclude the 
possibility of evaluating creative proposals using entirely novel 
technologies and approaches?  Genomics is a very fast-moving field.  
RFPs cannot hope to anticipate innovations even six months into the 
We understand that the root problems of the NRI stem from insufficient 
funding of the program by Congress.  We recognize our joint 
responsibility to address the problem at that level.  Nevertheless, we 
believe the restrictions in the RFP are not in the long-term interests of 
the program.  Any criteria which direct funding to special interests 
reduce the credibility of the program, which should base its decisions 
entirely on scientific merit.
Since the deadline for this program is still a ways off (June 15), we 
can see no reason why the RFP should not be modified for the 2006 
Dr. Thomas D. Kocher
On behalf of the additional signatories on the following page.
cc. Dr. Anna Palmisano
     Dr. Peter Burfening
     Dr. Muquarrab Qureshi

Additional signatories to the letter to Dr. Colien Hefferan:
Dr. Dennis Hedgecock, University of Southern California
Dr. John Liu, Auburn University
Dr. Greg Warr, Medical University of South Carolina