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United States Department of Agriculture

Agricultural Research Service

Research Project: Utilization of Genomics for Improving Production Traits in Cool and Cold Water Aquaculture

Location: Cool and Cold Water Aquaculture Research

2011 Annual Report


1a.Objectives (from AD-416)
1. Identify genes affecting variation in production traits in rainbow trout through QTL mapping and functional genomic (i.e. expression based) approaches. • 1.a. Detect and fine map quantitative trait loci for resistance to bacterial cold water disease in rainbow trout. • 1.b. Fine map quantitative trait loci affecting response to crowding stress. • 1.c. Identify genes affecting response to crowding stress through functional genomic approaches. • 1.d. Evaluate performance of fish differing in stress response phenotypes. • 1.e. Identify genes affecting carcass quality traits in rainbow trout. • 1.f. Identify and characterize key oocyte-expressed genes/microRNAs important for folliculogenesis and early development.

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.


1b.Approach (from AD-416)
The demand for seafood is increasing worldwide while captured fisheries harvest is limited and unsustainable. To meet increasing consumer demand, U.S. aquaculture producers have to achieve improved efficiencies and sustainable practices while maintaining and improving product quality. The application of genomic technologies towards the genetic improvement of aquaculture species is expected to facilitate selective breeding and provide basic information on the biochemical mechanisms controlling traits of interest. In collaboration with U.S. and international scientists, we have developed a suite of genome tools and reagents for rainbow trout to identify and characterize genes affecting aquaculture production traits. Projects concurrent with our previous 5-year project characterized the genetic variation of the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock with respect to resistance to Bacterial Cold Water Disease (BCWD) and response to crowding stress. Specific crosses were identified to facilitate the identification of genes affecting these traits through genetic mapping and functional genomic approaches. The current project will improve and utilize genome mapping approaches to identify positional candidate genes affecting these traits. This genetic information will be used for improving our understanding of the genetics of disease resistance and production traits and could be transferred to the US industry through improved germplasm. In addition, possibilities for developing informative crosses and functional genomic approaches which target the identification of genes affecting carcass quality traits will be determined. We will also continue to identify and characterize genes in the oocyte (pre-mature egg) which impact embryonic development and egg quality traits important to breeders.


3.Progress Report
All activities for this project are associated with efforts to understand, improve, and effectively use fish genomic resources (NP 106 Component 1). Progress towards Objective 1 included efforts to identify genes affecting the rainbow trout response to stress. Fish response to stress is an important factor in aquaculture production, having impacts on growth, feed efficiency, immune response, and reproductive characteristics. Efforts to identify the genes responsible for these effects included measuring plasma cortisol concentrations in response to crowding for three generations of a broodstock pedigree in combination with genetic marker analyses. In collaboration with the Genetics and Physiology Project, we detected quantitative trait loci (QTL) in the third generation of the NCCCWA pedigree broodstock which impact response to handling.

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.


4.Accomplishments
1. Construction of a comparative map for rainbow trout with model fish species. ARS researchers at the National Center for Cool and Cold Water Aquaculture (NCCCWA), Leetown, WV, have developed a suite of molecular tools for rainbow trout to enhance selective breeding of important aquaculture production traits. We identified similarity between the rainbow trout genome map and the genome sequences of the model fish species zebrafish and stickleback. This resource is useful for predicting which genes reside in regions of the rainbow trout genome that were observed to affect aquaculture production traits. Identification of genes that affect those traits will enhance the production of superior rainbow trout germplasm to benefit US producers and consumers.


Review Publications
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.

Last Modified: 11/23/2014
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