Population Genetics Analysis and Sex GWAS of Hemicentrotus pulcherrimus

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H. pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high Fis and low Ne, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise Fst, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus.