Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (<i>Plectropomus leopardus</i>)

Abstract

The leopard coral grouper (<i>Plectropomus leopardus</i>) is a species of significant economic importance. While artificial cultivation of <i>P. leopardus</i> has thrived in recent decades, the advancement of selective breeding has been impeded by the absence of comprehensive population genome data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing (depth ≥ 14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for <i>P. leopardus</i>, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity (<i>θπ</i>) and fixation index (<i>F<sub>st</sub></i>) in these four clusters. Moreover, by leveraging these high-coverage re-sequencing data, we successfully constructed the first haplotype reference panel specific to <i>P. leopardus</i>. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we used low-coverage sequencing data in conjunction with imputation for a genome-wide association study to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting <i>P. leopardus</i>.