Genome-wide association study for growth-related traits in golden pompano (Trachinotus ovatus)

Growth-related traits are complex and economically important traits in the aquaculture industry. Improvement of growth traits is generally considered as the main objective in breeding programs of farmed fish. The molecular basis underlying Golden pompano (Trachinotus ovatus) growth traits remains largely unknown. T. ovatus is a commercial marine fish species with a considerable market value. It is necessary to select new varieties of T. ovatus with fast growth traits, which could contribute to increased production and lower costs. In this study, the whole genome resequencing (WGS) was applied for genotyping 716 T. ovatus individuals and 4,886,850 high-quality single nucleotide polymorphism (SNP) located on 24 chromosomes were developed. A genome-wide association study (GWAS) was performed to detect SNPs and genes that are potentially related with growth traits, including body weight (BW) and body length (BL). Results indicated that 107 SNPs were significantly associated with growth traits, of which 18 SNPs were commonly shared with BW and BL traits. Furthermore, 108 genes were annotated by the identified SNPs. GO enrichment analysis suggested that the terms related with muscle growth, anabolism, and bone development were significantly enriched. Most candidate genes were known to be involved in muscle growth and bone development, some of which were reported to be associated with muscle hypertrophy in humans. This study provides useful information to understand the genetic architecture of growth-related traits and provides effective molecular markers for future genome-wide selection breeding of T. ovatus.