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From: "John Liu" []
To: "aquaculturegenomics" []
Cc: "Grant Burgess" []
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 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 .

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: .

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: 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 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, , Voice (703) 292-7184, Fax (703) 292-9064.q