ARS | Publication request: GENOMICS AND GENETICS:MOLECULAR VARIATION, BIOINFORMATICS AND FUNCTIONAL GENOMICS, IMPLEMENTATION INTO THE NCCCWA BREEDING PROGRAM

Submitted to: Meeting Abstract
Publication Type: Abstract
Publication Acceptance Date: January 24, 2006
Publication Date: February 16, 2006
Citation: Rexroad III, C.E., Palti, Y., Vallejo, R.L., Silverstein, J. 2006. Genomics and genetics:molecular variation, bioinformatics and functional genomics, implementation into the ncccwa breeding program. BARD Workshop: Aquaculture Genetics-Status and Prospects, Eilat, Israel. Meeting Abstract.

Technical Abstract: The USDA/ARS National Center for Cool and Cold Water Aquaculture is working to integrate molecular genetic technologies into a selective breeding program aimed at the genetic improvement of rainbow trout for aquaculture production efficiency. To date, much of our efforts have focused on the development of a diverse arsenal of genome tools and reagents which will be required to undertake this task. This includes the : 1) characterization of microsatellite genetic markers for genetic mapping, linkage disequilibrium mapping, and population genetic studies; 2) identification of expressed sequence tags to support candidate gene approaches and high-throughput functional genomics; and 3) construction of bacterial artificial chromosome libraries to conduct physical mapping, fine mapping, integration of cytogenetic and genetic maps, and large scale sequencing projects. The addition of these resources enhances our research programs and facilitates the development of new selective breeding strategies. Genetic mapping approaches traditionally target traits which are expensive or difficult to measure or require sacrificing fish. Loci influencing natural killer cell-like activity, temperature tolerance, spawning date, body weight, resistance to infectious pancreatic necrosis virus (IPNV), embryonic development rate, and albinism have been identified in rainbow trout. We have elected to target three traits due to their relevance to aquaculture production: stress tolerance (crowding stress measured by cortisol response), resistance to the bacterial pathogen Flavobacterium psychrophilum, and feed efficiency. Our approach includes the combination of genomics with traditional breeding strategies to identify and characterize loci (and eventually genes) responsible for genetic variation in NCCCWA broodstock. Identification of such loci will allow for use of marker/gene assisted selection in a multi-trait selection program where population genetic parameters are evaluated to achieve a balance of maximizing genetic gains without sacrificing genetic diversity to the point of negative impact. Employing molecular genetics in selective breeding programs enables the accumulation of vast amounts of molecular, phenotypic, and pedigree data for a broodstock population. Integration of these data into a meaningful breeding strategy is an essential task which requires the development of specialized bioinformatic tools. New molecular genetic and bioinformatic technologies must constantly be evaluated for their potential in increasing efficiency of selective breeding.