Construction of a Core Germplasm and Identification of Candidate SNPs Associated with Growth Performance of Epinephelus tukula by Whole-Genome Resequencing

Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data. The phenotypic traits of the individuals within the core collection were not significantly different from those in the original collection, suggesting effective representativeness of the core collection. Additionally, we performed genome-wide association study (GWAS) of E. tukula to identify candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits, to facilitate the improvements in the growth performance of this species. Twenty-six significant SNPs were identified, scattered among multiple chromosomes. Five SNPs were confirmed to be correlated with growth in another new group of 101 individuals. Based on the annotation results, these five SNPs were located in CCDC102A, NTRK2, CTSL, OTOF, and nestin, and were involved in cell development, differentiation and proliferation, glycolytic metabolism, neurological development, and myoblast differentiation. Our findings not only provide an effective basis for the conservation and utilization of E. tukula germplasm resources, but also promote the development of marker-assisted selection of E. tukula.