Genome-wide association study reveals growth-related SNPs and candidate genes in grass carp (Ctenopharyngodon idella)

Abstract

In China, the grass carp (Ctenopharyngodon idella) is a highly significant freshwater fish species. Enhancing growth-related traits can boost output, decrease costs, and accelerate the production of market-ready fish. In this study, the 21 K grass carp array was used to genotype 365 grass carp individuals, identifying 18,161 high-quality single nucleotide polymorphisms (SNPs) across 24 chromosomes. A genome-wide association study (GWAS) was conducted to detect SNPs and genes potentially associated with growth traits, including body height, body depth, body length, and body weight. We identified a strong positive genetic correlation (0.997–0.999) and a moderate to high heritability (0.421–0.501) among the three growth performance traits (body height, body depth, and body weight). Five SNPs, located on four chromosomes (LG01, LG05, LG07, and LG22), were identified as associated with growth-related traits. The proportion of phenotypic variance explained by these SNPs ranged from 6.3 to 13.5% for the growth-related traits. Two of these SNPs were associated with all traits, except body length. Additionally, 98 genes were annotated by the identified SNPs. Most of the candidate genes were known to be involved in muscle growth and bone development. Gene ontology enrichment analysis suggested that terms related to metabolic process and skeletal system morphogenesis were significantly enriched. This study offers insights into the genetic architecture of growth-related traits and provides effective molecular markers for future genome-wide selection breeding of grass carp.