NAGRP Aquaculture Genome Projects
7
From: John Liu [mailto:zliu@acesag.auburn.edu]
Sent: Wed, 21 Dec 2005 16:11:48 -0600
To: aquaculturegenomics@acesag.auburn.edu
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
http://www.intl-pag.org/14/14-aqua.html. Dr. Caird Rexroad is the
organizer for the Workshop, if you have any questions, please contact
Dr. Rexroad (CRexroad@ncccwa.ars.usda.gov).
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 (kltnbch@ag.arizona.edu). 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, http://www.csrees.usda.gov/ProgView.cfm?prnum=3D4467 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 mqureshi@csrees.usda.gov 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.
Sincerely,
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
apalmisano@csrees.usda.gov
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
(tdk@cisunix.unh.edu) 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
species.
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
profiling.
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
profiling!
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
future.
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
competition.
Sincerely,
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