Genetic diversity and population structure of different red swamp crayfish Procambarus clarkii populations across the north and south of China

We performed whole genome re-sequencing (WGS) of six crayfish populations across the north and south of China: Panjin (PJ), Liaoning province; Weishan (WS), Shandong province; Wuhu (WH), Anhui province; Jianhu (JH), Jiangsu province; Gehu (GH), Jiangsu province; Haikou (HK), Hainan province.A total of 120,906,91 high-quality single nucleotide polymorphisms (SNPs) were identified across the crayfish genome. The six geographical populations showed high level of diversity with the expected heterozygosity (He) ranged from 0.291 (WS) to 0.314 (PJ). The principal component and neighbor-joining (NJ) phylogeny analysis categorized the 180 individuals into three subgroups: the PJ and WS populations formed two separate subgroups, while the GH, JH, WH, and HK populations converged into a single subgroup. Moreover, the pairwise comparison of fixation index (Fst) values indicated a minor to moderate level of genetic differentiation among these populations, ranging from 0.0037 (GH, JH, WH & HK) to 0.0717 (WS & PJ), suggesting a greater genetic distance between the WS population and PJ population. Taken together, the SNPs identified in this study can serve as valuable genetic markers in future germplasm improvement of P. clarkii cultured stocks. These results will provide genetic information for further germplasm conservation and genetic improvement of P. clarkii.