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

Ali Ali,Mohamed Salem,Tim Leeds,Brett Kenney,Daniela Lourenco,Rafet Al-Tobasei

doi:10.1186/s12864-020-6617-x

Abstract

BackgroundGrowth 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.ResultsA previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, 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 a 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, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09).ConclusionThe 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.

Highlights

Growth is a major economic production trait in aquaculture
It is worth mentioning that a total of 90 fish from YC2010 were used in our previous study [18] to identify putative SNPs associated with muscle growth and quality traits (WBW, muscle yield, fat content, shear force, and whiteness index)
To make sure those fish do not interfere with the GWAS results, those 90 fish were excluded from the analysis in this study

Summary

Introduction

Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. Selective breeding improves heritable traits, taking advantage of existing genetic variation between individuals/families. Previous studies showed that selective breeding programs can improve animals’ bodyweights, Ali et al BMC Genomics (2020) 21:209 thereby contributing to increased aquaculture production [6, 7]. Selection on harvest weight can improve growth rate [8] and flesh color, and reduce production cost [9]. A family-based selection line for growth was established in 2002 at the USDA National Center for Cool and Cold Water Aquaculture (NCCCWA). More efforts are required to understand the genetic basis of bodyweight gain for genetically improved strains to achieve fast/efficient production [2]

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Conclusion