2010 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.
This report documents progress for 1930-31000-009-00D which started 12/14/2009 and continues research from 1930-31000-008-00D. In collaboration with scientists at the USDA/ARS MARC, we have developed protocols for analyzing large volumes of rainbow trout DNA sequence data using clonal fish lines. Current analysis protocols do not account for the recent trout genome duplication, which is causing incorrect assembly of DNA sequences.
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 gene responsible for this effect include cortisol measurements for three generations of a broodstock pedigree combined with genetic marker analyses. In collaboration with the Genetics and Physiology Projects, putative quantitative trait loci (QTL)were detected in the second generation (“F1”) of the NCCCWA pedigree broodstock which impact response to handling stress as measured by cortisol concentrations in the blood.
Spleen size index was previously shown to be correlated with resistance to Flavobacterium psychrophilum, a major disease concern for rainbow trout aquaculture. To identify genes affecting this trait spleen size was measured in two generations of a broodstock pedigree and genetic markers were used to scan the rainbow trout genome. In collaboration with the Fish Health Project, putative QTL in the NCCCWA broodstock were identified which impact spleen size.
A relational database integrating performance and molecular information facilitates the incorporation of data from diverse scientific disciplines and contributes for improving current methods for selective breeding in rainbow trout. In FY2010 2197 genetic markers from the NCCCWA genome studies were added to the database, table formats were created for fish genotypes and phenotypes and data uploaded for the NCCCWA genetic map panel, the stress QTL mapping panel and the spleen weight QTL mapping panel. Daily water use and temperature since 2005 and fish feed and liquid oxygen use data were also uploaded and interfaces for entering and modifying the data were created.
Mapping genes for bacterial disease resistance in rainbow trout: Bacterial cold water disease (BCWD) is caused by the bacterium Flavobacterium psychrophilum and is a major concern for rainbow trout aquaculture production and managers of recreational fisheries. Observation of this trait in three successive generations of NCCCWA broodstock identified that there are major genes which impact resistance to F. psychrophilum. This observation justifies the use of molecular approaches to enhance selective breeding strategies aimed at improving this trait in commercial populations.
Construction of the first genome-wide integrated genetic map for rainbow trout: ARS Scientists at the National Center for Cool and Cold Water Aquaculture (NCCCWA) at Leetown, WV have established a breeding program for rainbow trout with the aim of utilizing molecular genetic technologies to enhance selective breeding of important aquaculture production traits. This requires the development of species-specific molecular tools such as linkage maps which characterize inheritance of genetic markers and physical maps which contain overlapping DNA fragments from chromosomes. This year a comprehensive map integrating physical and linkage maps was constructed by connecting 274 reference points throughout the 29 chromosomes of the trout genome. This integrated mapping resource will be used to connect the inheritance of superior production traits with the genes which underlie them.
Wanna, W., Rexroad III, C.E., Yao, J. 2010. Identification of a functional splice variant of 14-3-3E1 in rainbow trout. Marine Biotechnology. 12:70-80.
Palti, Y., Luo, M., Hu, Y., Genet, C., You, F., Vallejo, R.L., Thorgaard, G., Wheeler, P., Rexroad Iii, C.E. 2009. A first generation BAC-based physical map of the Rainbow trout genome. Biomed Central (BMC) Genomics. 10:462.
Salem, M., Kenney, B.P., Rexroad Iii, C.E., Yao, J. 2010. Proteomic signature of muscle atrophy in rainbow trout. Journal of Proteomics. 73(4):778-789.
Sanchez Castano, C., Smith, T.P., Wiedmann, R.T., Vallejo, R.L., Salem, M., Yao, J., Rexroad Iii, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. Biomed Central (BMC) Genomics. 10:559.
Rexroad Iii, C.E., Vallejo, R.L. 2009. Estimates of linkage disequilibrium and effective population size in rainbow trout. BioMed Central (BMC) Genetics. 10:83.
Palti, Y., Gahr, S.A., Purcell, M.K., Hadidi, S., Rexroad III, C.E., Wiens, G.D. 2010. Identification, characterization, and genetic mapping of TLR7, TLR8a1 and TLR8a2 genes in rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology. 34:219-233.
Palti, Y., Rodriguez, M., Gahr, S.A., Purcell, M., Rexroad III, C.E., Wiens, G.D. 2010. Identification, characterization and genetic mapping of the TLR1 gene in rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology. 28:918-926.
Kongchum, P., Palti, Y., Hallerman, E., Hulata, G., David, L. 2010. SNP discovery and development of genetic markers for mapping immune response genes in common carp (Cyprinus carpio). Fish and Shellfish Immunology. 29:356-361.