Genetic diversity and population structure of the swimming crab (Portunus trituberculatus) in China seas determined by genotyping-by-sequencing (GBS)

Abstract

The commonly called swimming crab (Portunus trituberculatus) is widely distributed within the coastal waters of China and is a commercially important aquatic species due to its high edibility and rich nutrition levels. Previous studies based on P. trituberculatus population genetic diversity and structure were performed using molecular markers, especially microsatellite DNA. These studies only yielded a limited amount of genetic information. In this study, 270 samples from nine P. trituberculatus populations were collected from the coast of China. Genotyping-by-sequencing (GBS) technology was carried out to elaborate their genetic structures and differences between them. In total, 684.46Gb of clean data were generated, and 203,814 high-quality bi-allelic SNPs were identified following quality control. Based on these SNPs, diversity index analysis showed that all of the populations showed a similar, yet low, level of genetic diversity. The pairwise population differentiation index (Fst) ranged from 0.0016 to 0.0462 with an average of 0.0160, which revealed little genetic differentiation between the populations. Population structure, phylogenetic clustering and principal component analysis clustered all 270 individuals into three major groups and detected genetic connectivity with biological mixing among these samples. Collectively, these results will facilitate resource management and provide valuable SNP markers for germplasm improvement in stocks of P. trituberculatus.