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Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M. Cleveland, P. Brett Kenney, Roger L. Vallejo, Yniv Palti, Timothy D. Leeds
Frontiers in genetics 2016 v.7 no. pp. -
carcass weight, fish, carcass yield, Mus musculus, phenotype, genome-wide association study, genotyping, introns, body weight, models, chromosome mapping, growth performance, genetic variance, exons, single nucleotide polymorphism, fish culture, loci, breeding, Oncorhynchus mykiss, fish fillets, pedigree
Fillet yield (FY, %) is an economically important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has not received much attention in breeding programs because it is difficult to measure on a large number of fish and it cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. Here, we conducted a genome-wide association study (GWAS) for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a population of rainbow trout selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1,447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped using a high-density SNP array, were used in the GWAS analysis for FY, FW, and CAR. A total of 17,174 and 15,810 records from 789 families representing 7 generations were available for BW10 and BW13, respectively. Complete pedigree data were available dating back to initial development of the population (8 generations). A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. Two non-overlapping windows of 20 SNPs each located on chromosome Omy9 explained the largest proportion of the genetic variance for FY (1.5% and 1.0%) and FW (1.2% and 1.1%). One window on Omy5 explained 1.4% and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17 and Omy9 (the same window detected for FY) explained 1.7%, 1.7%, and 1.0%, respectively, of the genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the Mus musculus genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may have a significant effect on the variation in growth and fillet yield in rainbow trout.