Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Grazyella M Yoshida,José M Yáñez

doi:10.1186/s12864-020-07341-z

Grazyella M Yoshida, José M Yáñez

Open Access

https://doi.org/10.1186/s12864-020-07341-z

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Abstract

BackgroundBody traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits.ResultsA multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromis niloticus) using genotypes imputed to whole-genome sequences (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13 to 44%, depending on the trait analyzed. The better resolution of the WGS data, combined with the increased power of the mtGWAS approach, allowed the detection of significant markers which were not previously found in the stGWAS. Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively.ConclusionsThe high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

Highlights

Body traits are generally controlled by several genes in vertebrates, which in turn make them difficult to identify through association mapping
After quality control applied to the 50 K single nucleotide polymorphism (SNP) chip, 5905, 4114 and 3665 SNPs were removed by Hardy-Weinberg equilibrium (HWE), Minor allele frequency (MAF) and genotyping callrate filters, respectively, 29,587 SNPs remained for subsequent analyses
We found moderate to high heritability values for average daily gain (ADG), body weight at harvest (BWH), waste weight (WW), head weight (HW), head-on weight (HON), body length at harvest (BLH), fillet weight (FW) and fillet yield (FY), which is consistent with previous estimates for Nile tilapia calculated using pedigree and genomic methods [8, 9, 20, 21]

Summary

Introduction

Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. The most important body traits in Nile tilapia are body weight measured at a specific age (e.g. body weight at harvest), fillet weight or fillet yield (fillet weight/body weight). These traits show heritability values ranging from 0.06 to 0.48, when using pedigree-based estimates [3,4,5,6,7,8,9]. Previous studies have estimated high values of genetic correlations between harvest weight and fillet weight (> 0.96) and moderate to high values between harvest weight and fillet yield (0.21 to 0.74) [7, 9, 10], suggesting that is not possible to improve fillet traits independently of body weight [11]. Other body traits which have been proposed as selection criteria to generate more profitable commercial fish populations, are reduced waste (sum of bones, viscera, head, and fins) and carcass weight, due to their higher heritability values, less correlation to body weight, compared to fillet weight, and null or even favourable impact on fillet yield [13, 14]

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