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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #323549

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Genome-wide association study for identifying genome loci that affect fillet yield in rainbow trout (Oncorhynchus mykiss)

item GONZALEZ-PENA, DIANELYS - Oak Ridge Institute For Science And Education (ORISE)
item Leeds, Timothy - Tim
item Gao, Guangtu
item Vallejo, Roger
item Palti, Yniv

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2015
Publication Date: 1/10/2016
Citation: Gonzalez-Pena, D., Leeds, T.D., Gao, G., Vallejo, R.L., Palti, Y. 2016. Genome-wide association study for identifying genome loci that affect fillet yield in rainbow trout (Oncorhynchus mykiss) [abstract]. Plant and Animal Genome. P075.

Interpretive Summary:

Technical Abstract: Fillet yield (FY, %) is an economically important trait in rainbow trout aquaculture that reflects production efficiency. Despite that, FY has not received much attention in breeding programs because it is costly to measure and difficult to select on, limiting the genetic progress in traditional selection programs. The recent development of 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 using the synthetic population of rainbow trout developed at the National Center for Cool and Cold Water Aquaculture. The GWAS analysis was performed using the weighted single-step GBLUP method. Phenotypic records of 1,487 fish from ~ 300 full-sib families, in three successive generations, sacrificed at ~1.5 kg were analyzed with genotype data from 1,183 fish (875 with FY phenotypes and 308 non-phenotyped ancestors). A total of 38,107 effective SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects and animal as a random effect. Two non-overlapping windows of 25 SNPs located on chromosome Omy28 were responsible for 1.4% and 1.1% of the genetic variability for FY. Among the detected SNPs, 62% were in genes that participate in insulin binding, lipid metabolism homeostasis, cations channel activity, and ATP metabolism and 38% were near these genes. Further studies will evaluate the effects of these markers on growth performance and fillet quality in rainbow trout.