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United States Department of Agriculture

Agricultural Research Service

2008 Annual Report

1a.Objectives (from AD-416)
1) Continued development of a rainbow trout genetic map to reveal qualitative and quantitative trait loci affecting traits associated with aquaculture production. 2) Identification and characterization of genes affecting disease resistance, growth, and embryonic development through functional genomic technologies. 3) Development of strategies to implement functional genomic and genetic mapping information into the NCCCWA rainbow trout selective breeding program using bioinformatics. 4) Develop databases and programs to assimilate and coordinate genomic data on the rainbow trout broodstock developed at the NCCCWA. 5) Develop methodology to utilize rainbow trout genomic information in comparative analyses to identify potential critical functional genes and genetic pathways.

1b.Approach (from AD-416)
Aquaculture is the most rapidly growing segment of U.S. agriculture and the only sustainable option for satisfying the globally increasing demand for seafood products. Although demands in domestic and international markets remain high, the growth of the U.S. rainbow trout aquaculture industry has leveled off. In order to compete, U.S. trout farmers must overcome losses due to diseases and improve the growth characteristics of this species. A major constraint to increasing the production efficiency is the lack of genetically improved aquaculture stocks. One approach to address these problems is genetic improvement through selective breeding. NCCCWA has initiated a multidisciplinary approach to selective breeding of rainbow trout. Coordination of the activities proposed in this Project Plan with ongoing pathogenic disease research being conducted by project "Host, Pathogen, and Environmental Interactions in Cool and Cold Water Aquaculture" and growth, stress, and reproduction research being conducted by project "Utilizing Gentic for Enhancing Cool and Cold Water Aquaculture Production", will allow for the identification of genes affecting important aquaculture production traits. The result will be genome information which will allow for increased understanding of the biological mechanisms controlling these disease resistance, growth, stress, tolerance, and embryonic development and exploitation of positive genetic variation on the NCCCWA selective breeding program.

3.Progress Report
The ability of fish to respond to stress affects every aspect of the production cycle. To this end, the identification of genetic variation for traits associated with stress is critical to developing superior broodstock for the production environment. At NCCCWA we have selected fish containing genetic variation in stress response to crowding for an experiment aimed at identifying the genes underlying this response. This year we completed genotyping of 40 offspring from each of 12 crosses in an effort to identify chromosome regions affecting this trait. This project falls under National Program 106, Component 3, Genetic Improvement.

Increasing the number of genetic markers available for rainbow trout will facilitate our ability to conduct molecular biology research for this species. We targeted the development of single nucleotide polymorphism (SNP) markers to complement the current set of microsatellite markers used to construct the NCCCWA genetic map. In collaboration with the ARS Meat Animal Research Center, we sampled DNA from 96 unrelated fish representing the NCCCWA broodstock to identify over 10,000 putative SNPs which are in the process of validation. This project falls under National Program 106, Component 3, Genetic Improvement.

One caveat to using pedigree information in the NCCCWA selective breeding program is that our population has substructure. In other words, our founder generations contained individuals whose relatedness is not accounted for in our pedigree database initialized in 2002. We are evaluating the potential for molecular genetic data to replace or complement pedigree data for genetic analyses in aquaculture broodstock. Currently our simulated models suggest that the costs of genotyping would not provide significantly more useful information. This project falls under National Program 106, Component 3, Genetic Improvement.

Developing species-specific molecular tools such as chromosome maps is critical for identifying genes affecting production traits. In an effort to integrate the rainbow trout genetic and physical maps, the NCCCWA mapping reference families were genotyped for approximately 100 new microsatellite markers developed from the physical map. The integrated map will facilitate gene identification and characterization. This project falls under National Program 106, Component 3, Genetic Improvement.

Many genes involved in immune response to bacterial pathogens have been characterized across many species, including the gene family of the Toll-Like Receptors (TLR). This year we sequenced, mapped and determined the genomic structure and expression of the rainbow trout TLR1, TLR7, TLR8a and TLR8b genes. This project falls under National Program 106, Component 3, Genetic Improvement.

1. Construction of a physical map for the rainbow trout genome. The development of tools for molecular biology research in rainbow trout will facilitate our ability to conduct research in this species. To this end, recently we constructed a physical map of the entire rainbow trout genome by creating an assembly of small-overlapping DNA fragments. The new map includes two billion base pairs of DNA and represents 75% - 80% of the genome. This resource will facilitate identifying genes which affect important aquaculture production traits such as disease resistance. NP 106 (Aquaculture) component 3 (genetic improvement). Goal: 2. Initiate physical maps for aquaculture species; yielding integrated physical/genetic maps that serve as comprehensive maps for comparative mapping with whole genome sequences of model organisms.

5.Significant Activities that Support Special Target Populations

6.Technology Transfer

Number of the New MTAs (providing only)4

Review Publications
Salem, M., Silverstein, J., Rexroad III, C.E., Jianbo, Y. Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss). Biomed Central (BMC) Genomics. 8:328.

Qiu, G., Weber, G.M., Rexroad III, C.E., Yao, J. 2008. Identification of RtGST-1, a novel germ cell-specific mRNA-like transcript predominantly expressed in early previtellgenic oocytes in rainbow trout (Oncorhynchus mykiss). Molecular Reproduction and Development. 75:723-30.

Karlsson, S., Renshaw, M., Rexroad III, C.E., Gold, J. 2008. Pcr primer pairs for 100 microsatellites in red drum (sciaenops ocellatus). Molecular Ecology Notes. 8:393-398.

Pierce, L., Palti, Y., Silverstein, J., Barrows, F.T., Hallerman, E.M., Parsons, J.E. 2008. Evaluation of family growth response to fish meal and plant-based diets in rainbow trout (Oncorhynchus mykiss). Aquaculture. 278:37-42.

Ramachandra, R., Salem, M., Gahr, S.A., Rexroad III, C.E., Yao, J. 2008. Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development. Biomed Central (BMC) Genomics. 8:41.

Johnson, N., Vallejo, R.L., Silverstein, J., Welch, T.J., Wiens, G.D., Hallerman, E.M., Palti, Y. 2008. Suggestive association of major histocompatibility IB genetic markers with resistance to bacterial cold water disease in rainbow trout (Oncorhynchus mykiss). Marine Biotechnology. 10:429-437.

Schiotz, B.L., Jorgensen, S.M., Rexroad III, C.E., Gjoen, T., Krasnov, A. 2008. Transcriptomic analysis of responses to infectious salmon anemia virus infection in macrophage-like cells. Virus Research. 136:65-74.

Gahr, S.A., Vallejo, R.L., Weber, G.M., Shepherd, B.S., Silverstein, J., Rexroad III, C.E. 2008. Effects of short term growth hormone treatment on the rainbow trout (Oncorhynchus mykiss) liver and muscle transcriptomes. Physiological Genomics. 32:380-9.

Gahr, S.A., Rise, M., Hunt, P., Koop, B., Rexroad III, C.E. 2007. Characterization of expressed sequence tags from the pituitary of rainbow trout (oncorhynchus mykiss). Animal Biotechnology. 18(3):213-230.

Last Modified: 11/28/2014
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