Project Number: 1930-31000-009-00
Project Type: Appropriated

Start Date: Dec 14, 2009
End Date: Dec 13, 2014

Objective:
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.

Approach:
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.