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From: "John Liu" [liuzhan@auburn.edu]
To: "aquaculturegenomics" [aquaculturegenomics@acesag.auburn.edu]
Cc: "Grant Burgess" [Grant.Burgess@newcastle.ac.uk]
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 21
Date: Sun, 19 Dec 2008 14:43:53 -0500
Happy Holidays!
USDA releases AFRI Funding Programs: USDA releases its AFRI
Funding Programs. The Agriculture and Food Research Initiative (AFRI)
replaces the National Research Initiative (NRI). AFRI offers research,
education, extension project opportunities that focus on six key areas of
importance to agriculture, nutrition, food safety, environment, and rural
communities: 1. Plant Health and Production and Plant Products; 2.
Animal Health and Production and Animal Products; 3. Food Safety,
Nutrition, and Health; 4. Renewable Energy, Natural Resources, and
Environment; 5. Agriculture Systems and Technology; 6. Agriculture
Economics and Rural Communities. For more information, please visit
http://www.csrees.usda.gov/funding/afri/pdfs/program_announcement.pdf
The actual RFP will be released sometime in January 2009.
Geoff Waldbieser named Interim Coordinator for Catfish. Dr. Geoff
Waldbieser of USDA ARS Catfish Genetics Unit at Stoneville, Mississippi
has been named as Interim Coordinator for Catfish under the NRSP-8
Aquaculture. After collection of all nominations at PAG in San Diego, an
electronic vote will be conducted for the Catfish Coordinator. Dr. Melanie
Wilson of University of Mississippi Medical Center has been the
coordinator. Due to increases of her teaching responsibilities, she has to
make this change. Please join me to thank Dr. Wilson for her leadership
and great work in the last five years.
Aquaculture Workshop will be held Saturday - Sunday (January 10-11, 2009):
Dr. Yniv Palti has put together a great program. For program
details, please visit http://www.intl-pag.org/17/17-aqua.html .
The Aquaculture social and posters reception: will be held Saturday
evening as usual.
Aquaculture Genomics Travel Awards: The Aquaculture Species
Group is pleased to announce that the following have won the 2009
Aquaculture Genome Travel Award:
Elodie FLEURY, oyster
Takashi Koyama, shrimp
Cecilia Castaño Sánchez, salmonid
Artur B. Veloso, shrimp
Jessica Petersen, salmonid
Melinda Baerwald, salmonid
Shaolin Wang, catfish/oyster
Jason Abernathy, catfish
Hong Liu, catfish
Danielle Gorbach, shrimp
Jieying Li, salmonid
Yongping Wang, oyster
Liusuo Zhang, oyster
Haiyang Yu, oyster
Hong Yu, oyster
Join me to congratulate them for receiving the Travel Award. Considering
the small research community and the large number of species we are
working on, the Aquaculture Genome Executive Committee made special
efforts to bring as many graduate students and postdocs as possible to
the PAG Aquaculture Workshop.
NRSP-8 was renewed and the Genome Coordinators named. NRSP-8
was renewed for another 5 years beginning October 1, 2008 with a FY
2009 total budget of $500,000. A modest increase in budget was obtained
despite the fact that competition for multi-state research funding has
become increasingly intense, reflective of the past success of the NAGRP.
Special thanks go to Mary Delany of University of California-Davis for
leading the renewal proposal writing team and Muquarrab Qureshi, who
continues as Director, as well as all our CSREES administrative team.
Genome coordinators have been reappointed by the USDA-CSREES.
These now include John Liu and Caird Rexroad III, aquaculture; Juan
Medrano, cattle; Ernie Bailey, Horse; Jerry Dodgson and Hans Cheng,
poultry; Noelle Cockett, sheep; Max Rothschild, Swine; Jim Reecy and a
team of researchers (Sue Lamont, Chris Tuggle and Max Rothschild and
Shane Burgess), bioinformatics. Thank you for your support of me and
Caird Rexroad III to serve the community for the next five years.
BAC-based Physical map of rainbow trout available now: Dr. Yniv
Palti and colleagues have constructed the physical map of rainbow trout.
The WebFPC of the first generation assembly of the rainbow trout BAC
physical map is now available at:
http://www.genome.clemson.edu/activities/projects/rainbowTrout/index.shtml .
Tilapia genome update from Vertebrate Sequencing and Analysis
Team Broad Institute of MIT and Harvard: "the tilapia genome was
assigned by NHGRI to be sequenced by the Broad Institute. The current
switch to new sequencing technologies has required the Broad to enter a
development phase as we learn how to sequence and assemble genomes
using these new kinds of data. Unfortunately, this means that it is difficult
for us to give you a timeline as to when the tilapia genome will be
sequenced, as we are still uncertain how long it will take us to develop our
new assembly process. So do not think we have forgotten you - we are
just deep in our learning phase. In other news, the Broad has sequenced
156,216 BAC-end sequences from the VMRC-44 Tilapia BAC library using
the old Sanger sequencing technology. All the sequences are now
available through NCBI's trace archive and can be accessed through the
following search:
http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=CENTE
R_PROJECT%20%3D%20%22G1447%22&size=0&retrieve=Submit "
Oyster Genome Update: The Institute of Oceanology of Chinese
Academy of Sciences (IOCAS) and the Beijing Genomics Institute (BGI),
in collaboration with the international Oyster Genome Consortium (OGC),
have initiated a genome project for the Pacific oyster Crassostrea gigas.
The goal of the project is to produce a draft genome sequence of the
Pacific oyster to support gene discovery, evolutionary studies and
genome-based breeding. The project uses a combination of traditional
Sanger sequencing and the next generation sequencing technologies of
Illumina and 454 Life Sciences (Roche) for deep coverage and Sanger
sequencing of fosmid ends for connectivity. An inbred oyster furnished
the DNA to minimize potential problems with the high polymorphism
typical of marine invertebrates. Sequencing has begun at BGI and is
already close to finishing 50X coverage with Illumina sequencing. Initial
analysis of 30X coverage shows some problems with polymorphism, but
the results are comparable to those from other species. BGI is still
confident about the project. Dr. Guofan Zhang will present a preliminary
analysis at PAG XVII.
Oyster ESTs and Microarrays update: Fleury et al. have submitted a
manuscript for publication reporting the SIGENAE portal where ESTs
resulting from various European sequencing efforts will be publicly
available. This currently clusters 26,724 unique sequences, consisting of
8,885 contigs and 17,839 singletons. A cDNA microarray containing 9,058
unigenes was designed in Europe to identify genes differentially
expressed between lines selected to be resistant or sensitive to summer
mortality. Results are about to be submitted for publication by Fleury et al.
Elodie Fleury will participate in PAG XVII.
The JGI Oyster EST Project update: The JGI large-scale EST
sequencing project has so far produced 27,562 cDNA clone sequences
from larval and adult libraries. Another production run of the adult
libraries, which were made from the differentially tagged RNA of two
inbred lines, is expected to yield another 48,000 clone sequences.
Several hundred thousand EST sequences are being generated by 454
sequencing of two larval cDNA libraries.
The Oyster GIGASNP Project: USDA NRI Animal Genome Program has
funded a project, "GIGASNP: Genetic and physical mapping of the Pacific
oyster genome in support of an international sequencing initiative," which
was submitted by Dennis Hedgecock, Pat Gaffney, and Ximing Guo. The
primary goal of this project is to provide critical resources needed to
assemble the draft sequence of this highly polymorphic large genome
(824 Mbp). From EST sequences produced by the Joint Genome Institute
(DOE), the project will develop high quality coding SNP sequences,
validate their amplification from genomic DNA, and genotype >3000
candidate SNP markers by multiplex assays in four mapping families and
a panel of oysters from diverse stocks and closely related species. A
secondary goal is to identify 1500 SNP markers that are evenly spaced
across the genetic map and polymorphic enough to be broadly useful to
our international community. The project will also assign 500 mapped
SNPs to BAC clones by PCR, linking genetic and physical maps, and
develop a cytogenetic map by fluorescence in situ hybridization of mapped
BACs and selected repetitive elements. Integrated genetic, physical, and
cytogenetic maps are critical resources for bridging gaps in the draft
genome sequence.
Funding opportunity message from our friend, Dr. Greg Warr: As
some of us may know, our friend Dr. Greg Warr of Medical University of
South Carolina has recently started to serve as Program Director, Cellular
Systems Cluster, Molecular and Cellular Biosciences at NSF. The
following funding opportunity may interest you: " We are pleased to call
your attention to the newly released program announcement for the
Partnerships in International Research and Education (PIRE) program of
the National Science Foundation's Office of International Science &
Engineering (NSF/OISE). The PIRE program will support projects that 1)
undertake frontier research that cannot be done without the unique and
complementary contributions of both the U.S. and international partners, 2)
help develop a globally engaged U.S. science/engineering workforce,
AND 3) facilitate strengthened involvement by U.S. institutions in mutually
beneficial international research and education collaborations. The PIRE
program announcement number is NSF 09-505. A link to the program
announcement as well as additional information, including links to
abstracts of 32 active PIRE awards, can be found at
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=12819. PIRE is a
two-stage competition, beginning with required preliminary proposals,
which are due on February 26, 2009. U.S. universities that granted one or
more Ph.D.s in a science or engineering field since 2006 are eligible to
submit preliminary proposals. Each eligible institution may submit up to
three preliminary proposals. Researchers may be involved as PI, co-PI,
senior personnel, consultant or subawardee on no more than one
proposal. PIRE awards support the U.S. side of the international
collaboration. The Biological community has done well in past
competitions and we wish to encourage submissions to this competition.
For further information, please contact: William J. Resetarits, Program
Director, Ecological Biology Cluster, Division of Environmental Biology,
National Science Foundation, 4201 Wilson Blvd., Suite 635,
wresetar@nsf.gov , Voice (703) 292-7184, Fax (703) 292-9064.q