2008 Annual Report
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.
5.Significant Activities that Support Special Target Populations
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.