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Brief Summary of Minutes
The regional project NE-186: Genetic Maps of Aquaculture Species was originally approved to be a three year project that is now extended for two more years till December 31, 2004. Its goal is to develop moderate-density genetic linkage maps of highly polymorphic DNA markers, mapping of quantitative trait loci, and initiating comparative genome mapping for five important aquaculture species (catfish, salmonids, tilapia, shrimp, and oyster).
Good progress has been made in this reporting period. Because this project involves a large number of researchers from various institutions including universities, government research agencies, and private organizations, a thorough summary of detailed research progress can be difficult. This project also involves a good level of international collaborations from many nations. For the most part, detailed research results are available from published papers, information stored in databases, or on searchable web pages.
An annual Aquaculture Genomics Workshop was held in San Diego along with the Plant and Animal Genome Conference. Over 60 scientists participated in the Workshop . A total of 19 scientists made oral presentations and 24 posters were presented. Students travel awards were made to three recipients: Arif Kocabas from Auburn University, C. Araneda Tolosa from Chile, and K. Nakamura from Japan. The Workshop also invited Dr. Richard Frahm and Dr. Peter Brayton to present lectures on funding opportunities in the USDA.
A business meeting was held to discuss several issues: First, the next years Workshop organizer was determined to be Dr. Acacia Alcivar-Warren. The pros and cons of joining the NRSP-8 were discussed. A vote was taken and the majority was in favor of joining NRSP-8 (which later was approved by voting of the NRSP-8 committee). A reception was held in the evening to conclude the Workshop.
Since the effort of joining as part of NRSP-8 was after the Workshop, Dr. Bill Trumble, the Administrative Supervisor of this regional project, and Dr. John Liu, the annual Workshop organizer, made presentations on behalf of the Aquaculture Genomics group on our proposal of joining the NRSP-8 to the NRSP-8 committee. Discussions were conducted in the committee with much support. The NRSP-8 Committee voted and approved Aquaculture as one species group in joining the NRSP-8. Dr. Liu was nominated as interim species coordinator within NRSP-8 who in turn nominated Dr. Pat Gaffney and Dr. Caird Rexroad as members of the Writing Committee for the renewal of the NRSP-8 proposal.
Accomplishments
Genetic linkage maps of moderate density were constructed for tilapia, salmonids, catfish, oyster, and shrimp. The most comprehensive linkage map is the genetic linkage of salmonids. Through collaboration of a large number of researchers in the U.S. (e.g., Dr. Gary Thorgaard and Dr. Ruth Phillips at Washington State University, Dr. Caird Rexroad at the National Cold and Cool Water Aquaculture Center, Dr. John Killefer at West Virginia University, Dr. William Young at Northern Arizona State University, etc), Canada (e.g., Dr. Moira Ferguson at University of Guelph, and many others involved in the Canadian Salmonids Genome Initiative), Norway, and several other nations, integrated genetic linkage maps of salmonids are evolving with large numbers of polymorphic markers. Research on improving the linkage maps of tilapia, catfish, oyster, and shrimp are progressing rapidly with more markers being mapped using microsatellites, AFLP, and other markers. Research activities in development of polymorphic markers, particularly type I molecular markers are keen. For instance, laboratories of Dr. Kim Reece at Virginia Poly Tech Institute and State University, Dr. Patrick Gaffney at University of Delaware, and Dr. Ximin Guo at Rutgers University have made important advances in molecular marker development. In collaboration with Genomar in Norway, Dr. Thomas Kochers laboratory has produced genetic linkage maps of tilapia using both microsatellites and AFLP markers. In catfish, laboratories of Dr. John Liu at Auburn University and Dr. Geoff Waldbieser at ARS USDA National Warm Water Aquaculture Center have constructed genetic linkage maps using both microsatellite and AFLP markers. In case of catfish, linkage maps have been constructed using both channel catfish intraspecific resource families as well as channel catfish x blue catfish interspecific resource families. While intraspecific mapping resources are important for genetic considerations in crossbreeding, interspecific mapping resources are important for interspecific hybridization and introgression. <br />
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<br>Initial efforts have been devoted to mapping quantitative trait loci (QTL) in aquaculture species. For instance, Dr. X. Guos laboratory reported their results in searching for genes involved in host defense against Perkinsus marinus and Haplosporidium nelsoni infections in Eastern and Pacific oysters; Dr. Ferguson reported comparative mapping of QTLs in salmonids fishes; Dr. Greg Warrs group in South Carolina reported results of functional analysis of antiviral immunity in shrimps; Dr. Kochers laboratory reported progress in QTL mapping in tilapia; Dr. John Liu reported results of QTL mapping in catfish.<br />
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<br>Much effort has been devoted in development of genomic reagents such as expressed sequenced tags (ESTs) and bacterial artificial chromosome (BAC) large-insert libraries. Thousands of ESTs have been developed from catfish (John Liu and Geoff Waldbieser), salmonids (John Killefer and Caird Rexroad), oysters (Greg Warr, Paul Gross et al. et Medical University of South Carolina; Pat Gaffney), and shrimps (J. Xiang from China, Acacia Alcivar-Warren at Tufts University). These ESTs will be important genomic resources for the development of type I molecular markers, and for the development of cDNA microarrays. A tilapia BAC library was reported by Dr. Tom Kochers lab, which is being fingerprinted for production of contigs. Two BAC libraries were constructed from catfish; one by Dr. Pieter de Jong (Oakland Childrens Hospital) and the other by Dr. Waldbiesers group. <br />
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<br>Great progress has been made on functional analysis of genes and their functions. Using a Lynx high tech analysis, Dr. Dennis Hedgecock at the University of California-Davis has examined gene expression profiles for the analysis of hybrid vigor in oysters; microarrays has been used for the analysis of differentially expressed genes during cold acclimation in catfish (John Liu). <br />
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<br>An annual Aquaculture Genomics Workshop was held in San Diego along with the Plant and Animal Genome Conference. Over 60 scientists participated in the Workshop . A total of 19 scientists made oral presentations and 24 posters were presented. Students travel awards were made to three recipients: Arif Kocabas from Auburn University, C. Araneda Tolosa from Chile, and K. Nakamura from Japan. The Workshop also invited Dr. Richard Frahm and Dr. Peter Brayton to present lectures on funding opportunities in the USDA. <br />
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Publications
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Impact Statements
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