Genome-wide identification of loci associated with growth in rainbow trout

Abstract

Background Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout.Results A 50K, gene-transcribed SNP chip was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 46 SNPs were identified in association with bodyweight gain. The highest SNP associated with this trait was identified in a gene coding for thrombospondin-1 (THBS1) (R 2 = 0.09).Conclusion The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.

Genome-Wide Scan For Common Variants Associated With Intramuscular Fat And Moisture Content In Rainbow Trout

“…Aguilar et al (2019) showed that the highest peak based on the p-value was not the same based on the proportion of variance explained, and this is because the latter depends on allele frequency, i.e., high effect but low frequency decreases the variance explained [97]. This result is consistent with other studied traits, such as fillet firmness, protein content [20], and bodyweight gain [98] in rainbow trout.…”

Genome-Wide Scan for Common Variants Associated With Intramuscular Fat and Moisture Content in Rainbow Trout

“…Increased knowledge of the genetic basis of muscle quality traits will facilitate to advance the commercial breeding in salmonids. GWA studies are powerful tools to identify genetic variants associated with complex traits [36,39,40].…”

“…A 50K transcribed SNP-chip, suitable for GWA analyses, has been recently developed in our laboratory. The array has been used to identify large-effect QTL responsible for genetic variance in fillet yield, firmness, protein content, and body weight gain using the same fish population used in this study [36,39,40]. The current study aimed to identify QTL associated with the additive genetic variance in fillet fat and moisture content for the same rainbow trout population.…”

Genomic Predictions for Fillet Yield and Firmness in Rainbow Trout Using Reduced-density SNP Panels

“…The selective breeding program has been established in 2004 and underwent five generations of selection for body weight. Details on how the population was formed and selected for growth can be found in [8,54]. The trimmed fillet was weighed, and fillet yield was calculated as a percent of whole-body weight.…”