Genetic Diversity and Population Structure of Macrobrachium nipponense Populations in the Saline–Alkaline Regions of China

The oriental river prawn <i>Macrobrachium nipponense</i> is of great economic importance in China. However, its culture in the saline-alkaline regions is limited. This study used D-loop region sequences to analyze the genetic diversity and population structure across the saline-alkaline regions of China. A total of 264 individuals were successfully sequenced from nine sites, including Daqing in Heilongjiang Province (HLJ), Songyuan in Jilin Province (JL), Ulanhot in the east of inner Mongolia (NMG), Jingtai in Gansu Province (GS), Dongying in Shandong Province (SD), Dongtai in Jiangsu Province (JS), Nanchang in Jiangxi province (JX), Tianjin in mainland China (TJ), and Yinchuan in Ningxia Province (NX). In addition, 89 haplotypes were defined. The haplotype diversity (<i>h</i>) and nucleotide diversity π showed remarkable genetic diversity in the JS, NX, JL, and TJ sites. It was found that the genetic variation within sites was relatively greater. The genetic distance (D) and the pairwise genetic differentiation index (F_ST) revealed that SD and GS are closely related. The F_ST values among the nine sites were significant except for the one between SD and HLJ (<i>p</i>-value > 0.05). The cluster analyses and the phylogenetic tree identified two main groups. There is an association among sites by geographic location, and the JS site shows higher diversity. The results of this study provide basic information for the protection and development of <i>M. nipponense</i> resources in the saline-alkaline regions of China.