Location: Cool and Cold Water Aquaculture Research
2011 Annual Report
2: Develop genomic tools and resources to facilitate the use of state of the art approaches for genetic improvement of rainbow trout. • 2.a. Facilitate the identification of genes affecting production traits by producing a second generation bacterial artificial chromosome (BAC) map which is anchored to the genetic map. • 2.b. Develop single nucleotide polymorphic (SNP) markers to enhance fine mapping and enable genomic selection for rainbow trout. • 2.c. Identification of microRNAs that affect expression of genes controlling production traits in rainbow trout.
3: Develop database to store, and facilitate analysis of genotypic and phenotypic data.
Progress towards Objective 2 included efforts to develop high throughput protocols for mapping genes affecting traits associated with aquaculture production efficiency. To this end, a collaboration with scientists from the University of Oregon was initiated to implement protocols for next-generation sequencing of Restriction-site Associated DNA (RAD) tags into our QTL mapping studies. The new protocols have been demonstrated to increase the density of the rainbow trout genetic map to approximately 5,000 markers in a rapid and cost effective manner. Previous medium density genetic maps for rainbow trout contained approximately 1,000 genetic markers. The new technology will enable more robust and accurate mapping of genes that affect aquaculture production traits. A second approach to identifying genes affecting stress response includes sequencing of mRNAs from fish subjected to sub-lethal extremes of high temperature, low temperature, salinity, crowding, and a combination of low levels of dissolved oxygen/high levels of carbon dioxide. To this end mRNA from gill, brain, liver, spleen, kidney and muscle containing representative samples from all the different stressors was sequenced with 454 pyrosequencing to produce 3,160,306 high quality reads of which 2,326,354 were assembled into 110,026 contigs. Comparisons with existing transcriptome data reveal a significant contribution to publicly available transcriptome data for rainbow trout. This resource will be used in future studies for global characterization stress responses at the level of the transcriptome.
Vallejo, R.L., Wiens, G.D., Rexroad III, C.E., Welch, T.J., Evenhuis, J., Leeds, T.D., Janss, L.L., Palti, Y. 2010. Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis. Journal of Animal Science. 88:3814-3832.
Salem, M., Rexroad III, C.E., Wang, J., Thorgaard, G.H., Yao, J. 2010. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. Biomed Central (BMC) Genomics. 11:564.
Kongchum, P., David, L., Hallerman, E., Hulata, G., Palti, Y. 2011. Molecular cloning, characterization and expression analysis of TLR9, MyD88 and TRAF6 genes in common carp (Cyprinus carpio). Fish and Shellfish Immunology. 30: 361-371.
Wang, J., Salem, M., Kenney, P., Rexroad III, C.E., Yao, J. 2011. Molecular characterization of the MuRF genes in rainbow trout: potential role in muscle degradation. Comparative Biochemistry and Physiology. 158(3):208-215.
Kongchum, P., Sandel, E., Lutzky, S., Hallerman, E., Hulata, G., David, L., Palti, Y. 2011. Association between IL-10a SNPs and resistance to cyprinid herpesvirus-3 infection in common carp (Cyprinus carpio). Aquaculture. 315(3-4):417-421.
Genet, C., Dehais, P., Palti, Y., Gavory, F., Wincker, P., Quillet, E., Boussaha, M., Gao, G. 2011. Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. Biomed Central (BMC) Genomics. 12:314.
Palti, Y., Genet, C., Luo, M., Charlet, A., Gao, G., Hu, Y., Castano-Sanchez, C., Yao, J., Vallejo, R.L., Rexroad III, C.E. 2011. A first generation integrated map of the rainbow trout genome. Biomed Central (BMC) Genomics. 12:180. DOI: 10.1186/1471-2164-12-180.
Castano, C., Palti, Y., Rexroad III, C.E. 2011. SNP analysis with duplicated fish genomes: differentiation of SNPs, paralogous sequence variants and multi-site variants. In: Liu, Z.J., editor. Next Generation Sequencing and Whole Genome Selection in Aquaculture. 1st edition. Malden, MA: Wiley-Blackwell. p. 133-150.
Aussanasuwannakul, A., Kenney, P., Brannan, R.G., Slider, S.D., Salem, M., Yao, J. 2010. Relating instrumental texture, determined relating instrumental texture, determined attachments, to sensory analysis of rainbow trout, Oncorhynchus mykiss, fillets. Journal of Food Science. 75:S365-S374. DOI: 10.1111/j. 1750-3841.2010.01770.x.