Identification of SNPs and candidate genes associated with early growth in orange-spotted grouper (Epinephelus coioides) by a genome-wide association study

Abstract

Orange-spotted grouper, Epinephelus coioides is one of the most economically important marine fish in the South China Sea. Exploring of the genetic basis controlling for the growth-related traits is helpful for the genetic breeding of the grouper. To date, the quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) that associated with early growth in the orange-spotted grouper are unclear. In this study, dissection of the genetic architecture of the early growth-related traits (body weight, body length and body height) were carried out for 288 orange-spotted groupers at 3 months post hatching by using an selective phenotyping-based genome-wide association study (GWAS). 5279 high-quality SNPs were identified for the population. A total of 11 SNPs that located on three chromosomes (Chr1, Chr9 and Chr22) were significantly associated with early growth-related traits. The proportion of phenotypic variance explained for these SNPs ranged from 5.15% to 6.89% for body weight, 5.23% to 6.95% for body length, and 5.29% to 6.21% for body height. Five of these SNPs were associated with all traits, and 3 SNPs were associated with body weight trait and body height trait. Based on these associated SNPs, some important candidate genes (e.g., mustn1, bmp7, sema3a, magi2, prkcd, capzb, twf2 and eps8l2) were predicted. To assess the reliability of candidate SNP datasets identified by GWAS analysis, we further verified the SNPs by using Sanger sequencing technology. This study provides important insights into the genetic basis of early growth-related traits in the orange-spotted grouper.