Genome-wide association analysis identifies genetic variants associated with muscle fatty acids and amino acids in grass carp (Ctenopharyngodon idella)

The composition and content of fatty acids (FAs) and amino acids (AAs) are important nutritional and sensory traits in aquaculture fish. To meet increasing demand while retaining quality, genetic selection in breeding programs is urgently needed to improve these traits. In this study, we performed the genome-wide association study (GWAS) to identify genetic variants and candidate genes potentially linked to FA and AA compositions in grass carp muscle. We focused on key dietary components, including unsaturated FAs and essential AAs. Through profiling of total FA and AA contents, we identified strong positive correlations among the compositions of most FAs and AAs. From our GWAS panel, 4,913,199 high-quality single nucleotide polymorphisms (SNPs) were identified across the genome, of which 32 SNPs linked to 18 candidate genes were significantly associated with FA levels, and 202 SNPs linked to 115 candidate genes associated with AA contents. In addition, we categorized our sequencing population by region and detected allele frequencies of SNPs across four geographic locations. Notably, four FA-associated SNPs and 28 AA-associated SNPs exhibited geographic specificity. These results offered valuable insights into the complex genetic basis of FA and AA metabolism and deposition. Furthermore, this work provides potential genetic markers for selective breeding aimed at enhancing flesh quality in the economically important fish species, grass carp.