Genome-wide association study of key economic traits based on a 40K SNP array in spotted sea bass (Lateolabrax maculatus)

As an important marine aquaculture fish species in China, the increasing scale of spotted sea bass ( Lateolabrax maculatus ) farming has created a growing demand for superior germplasm resources. To meet the need for selective breeding, this study utilized the independently developed “Sea Bass No.1” 40K liquid breeding array to genotype 150 individuals from a selected spotted sea bass population. This yielded 41,535 high-quality SNPs. A genome-wide association study (GWAS) was then conducted to analyze the underlying genetic basis of growth traits, gut microbiota diversity metrics, and fatty acid traits. Heritability and correlation analyses indicated that growth traits and fatty acid traits are difficult to improve simultaneously through selection. Population structure analysis revealed a certain degree of stratification, with relatively distant kinship among individuals. GWAS revealed 31, 35, and 124 significant SNPs associated with growth, gut microbiota, and fatty acid traits, respectively. These SNPs were annotated to 225 candidate genes (37, 40, and 148 genes per trait, respectively), including key genes such as pkcϵ , gdf10-like , slc28a3 , kif , erβ , cdk5 , and pgc-1α . Enrichment analysis of the candidate genes revealed that the candidate genes were primarily involved in key biological pathways, including lipid metabolism, neural signaling, growth and development, and immune response. This study lays a foundation for the fine mapping of functional genes controlling key economic traits and for the implementation of genomic selection breeding programs.