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

Abstract

Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and 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. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 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, were used in the GWAS analysis. 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. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0-1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. 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 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of 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 affect variation in growth and fillet yield in rainbow trout.

Keywords: fillet yield; gene network; genome-wide association study; genomic selection; linkage map; rainbow trout; single-step GBLUP.

Figure 1

The proportion of genetic variance explained by 20-SNP regions for fillet yield.

Figure 2

The proportion of genetic variance explained by 20-SNP regions for fillet weight.

Figure 3

The proportion of genetic variance explained by 20-SNP regions for 10-month body weight.

Figure 4

The proportion of genetic variance explained by 20-SNP regions for 13-month body weight.

Figure 5

The proportion of genetic variance explained by 20-SNP regions for carcass weight.

Figure 6

Network of genes and neighboring genes in the same scaffold as the SNPs identified in the wssGWAS in windows responsible for ~1.0% or more of the total genetic variance of the analyzed traits. Green nodes denote genes and near genes detected by the wssGWAS analysis and pink nodes denote connecting neighbors. Edges denote known relationships between genes in the SysBiomics repository. Framed genes (red square) are discussed in the manuscript.