Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data

Abstract

Through imputation of genotypes, genome-wide association study (GWAS) and genomic prediction (GP) using whole-genome sequencing (WGS) data are cost-efficient and feasible in aquaculture breeding schemes. The objective was to dissect the genetic architecture of growth traits under chronic heat stress in rainbow trout (Oncorhynchus mykiss) and to assess the accuracy of GP based on imputed WGS and different preselected single nucleotide polymorphism (SNP) arrays. A total of 192 and 764 fish challenged to a heat stress experiment for 62 days were genotyped using a customized 1 K and 26 K SNP panels, respectively, and then, genotype imputation was performed from a low-density chip to WGS using 102 parents (36 males and 66 females) as the reference population. Imputed WGS data were used to perform GWAS and test GP accuracy under different preselected SNP scenarios. Heritability was estimated for body weight (BW), body length (BL) and average daily gain (ADG). Estimates using imputed WGS data ranged from 0.33 ± 0.05 to 0.55 ± 0.05 for growth traits under chronic heat stress. GWAS revealed that the top five cumulatively SNPs explained a maximum of 0.94%, 0.86% and 0.51% of genetic variance for BW, BL and ADG, respectively. Some important functional candidate genes associated with growth-related traits were found among the most important SNPs, including signal transducer and activator of transcription 5B and 3 (STAT5B and STAT3, respectively) and cytokine-inducible SH2-containing protein (CISH). WGS data resulted in a slight increase in prediction accuracy compared with pedigree-based method, whereas preselected SNPs based on the top GWAS hits improved prediction accuracies, with values ranging from 1.2 to 13.3%. Our results support the evidence of the polygenic nature of growth traits when measured under heat stress. The accuracies of GP can be improved using preselected variants from GWAS, and the use of WGS marginally increases prediction accuracy.

Keywords: GWAS; accuracy; genomic predictions; heat stress; rainbow trout; whole‐genome sequence.

FIGURE 1

Manhattan plot of percentage of genetic variance explained by each SNP using the wssGBLUP approach for (a) average daily gain, (b) body length and (c) body weight under chronic upper‐thermal stress in rainbow trout

FIGURE 2

(a) Accuracy of selection using pedigree BLUP (PBLUP), whole‐genome sequence (WGS) and different densities of genotype subsets (50K_pruned, 50K_wssGBLUP and 1K_wssGBLUP). (b) Relative increase in accuracy (%) of genomic selection using imputed WGS and different densities of genotype subsets (50K_pruned, 50K_wssGBLUP and 1K_wssGBLUP) compared with PBLUP for growth traits under chronic upper‐thermal stress in rainbow trout