Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2009
Publication Date: 12/14/2009
Citation: 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.
Interpretive Summary: The USDA/ARS National Center for Cool and Cold Water Aquaculture (NCCCWA) has established a breeding program for rainbow trout, the use of molecular genetic technologies in this program is expected to enhance capabilities for the selective breeding of important aquaculture production traits. To this end we have worked within international collaborations to develop genomic tools and technologies for rainbow trout while concurrently initiating and characterizing our broodstock population with respect to genetic and phenotypic variation relevant to aquaculture production. We report our characterization of linkage disequilibrium in the NCCCWA rainbow trout broodstock population, our results indicate that many genetic analyses will require significantly more molecular markers than currently exist for this species. Therefore, NCCCWA must continue to develop markers such as single nucleotide polymorphisms for use in identifying genes affecting important production traits.
Technical Abstract: The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To this end, the extent of LD has been characterized for humans and several agriculturally important livestock species including cattle, sheep, chickens, and pigs. All of these results indicate that large numbers of markers from high-density maps are required to identify genes of interest using whole genome association studies in these species. Characterizing the extent of LD in the NCCCWA rainbow trout broodstock population will enable the use of integrated mapping approaches and facilitate the identification of genes affecting traits of interest by determining the required marker density to perform genome wide association scans.