Genetic structure and selective signatures revealed by whole genome sequencing in potato grouper (Epinephelus tukula)

Epinephelus tukula exhibits both rapid growth and strong environmental adaptability, thereby serving as a widely employed broodstock in grouper aquaculture. However, in practical production, the genetic background of E. tukula remains poorly characterized, and the genetic relationships among individuals have not been adequately considered. To date, no studies have reported on the genetic diversity or selection signatures of E. tukula in aquaculture. Based on this, the present study utilized whole-genome sequencing data from 202 E. tukula individuals across multiple farms in different regions of Hainan Province to investigate population structure, genetic diversity, and genomic variations. Ancestral estimation and phylogenetic analysis successfully divided 169 of 202 E. tukula individuals into 10 distinct genetic populations. These populations exhibited low genetic diversity, with nucleotide diversity (π) values ranging from 2.53 to 3.06 × 10− 4. The range of fixation indices (FST) among populations was 0.060–0.153. Linkage disequilibrium (LD) decay rate and runs of homozygosity (ROHs) indicated that certain population likely underwent multiple rounds of artificial breeding, whereas others experienced less artificial breeding. By integrating two methods (XP-EHH and FST), we identified selection signals across these populations. Functional enrichment analysis highlighted 184 development-related genes as potential importance for future breeding efforts. Allele frequency analysis of selected SNPs in these genes across populations revealed that targeted artificial breeding can influence nucleotide diversity in development-related genes. Whole-genome sequencing provided high-quality data for dissecting the genetic structure of E. tukula populations in Hainan Province. Genomic selection sweep identified candidate regions and genes associated with important traits. This study enhances our understanding of the population genetics and selection signatures in E. tukula, and offers valuable insights for germplasm resource management and molecular -assisted breeding in E. Tukula.