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Genetic Diversity and Population Structure of Wild Macrobrachium nipponense in the Pearl River Basin: A Treasury of Germplasm for Aquaculture and Conservation
by
, , , ,
Hao Dong
1
,
Xiaofan Fang
1,
Yuefan Zhang
1,
Shubo Jin
1,2,3,
Wenyi Zhang
2,3,
Yiwei Xiong
2,
Hui Qiao
1,2,3 and 
Sufei Jiang
1,2,3,* 1
Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
2
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
3
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
*
Author to whom correspondence should be addressed.
Animals 2026, 16(18), 2869; https://doi.org/10.3390/ani16182869
Submission received: 7 August 2026
/
Revised: 8 September 2026
/
Accepted: 10 September 2026
/
Published: 11 September 2026
(This article belongs to the Section Aquatic Animals)
Simple Summary
The oriental river prawn (Macrobrachium nipponense) is an important freshwater aquaculture species in China. However, the genetic characteristics of wild populations distributed throughout the Pearl River Basin remain poorly understood. In this study, wild M. nipponense populations were collected from 14 locations across the Pearl River Basin, and mitochondrial DNA sequences were analyzed to investigate genetic diversity and differentiation among populations. The results showed that wild populations in the Pearl River Basin harbor high levels of genetic variation and exhibit clear genetic differentiation among populations from different geographic regions. Several populations showed distinctive genetic characteristics and may represent valuable genetic resources for conservation and breeding. This study provides important information for the conservation and sustainable utilization of wild M. nipponense populations and may contribute to the development of improved aquaculture strains in the future.
Abstract
This study evaluated the genetic diversity and population structure of wild M. nipponense populations in the Pearl River Basin based on mitochondrial DNA (mtDNA) D-loop sequences. A total of 14 wild populations were collected from the West River, North River, and Pearl River Delta, and genetic diversity and population differentiation were assessed using haplotype analysis, analysis of molecular variance (AMOVA), pairwise FST, and principal component analysis (PCA). A total of 351 variable sites were identified. The overall haplotype diversity (h) and nucleotide diversity (π) were 0.947 and 0.03665, respectively, indicating high genetic diversity across the Pearl River Basin. Significant genetic differentiation was detected among populations (FST = 0.3785, p-value < 0.001), with 37.85% of genetic variation occurring among populations. PCA revealed distinct genetic relationships among populations, supporting the presence of population genetic structure within the Pearl River Basin. Populations from Tian’e County, Xilin County, Dahua Yao Autonomous County, and other upper tributaries of the West River exhibited distinct genetic characteristics compared with populations from Zhaoqing City, Guiping City, Guangzhou City, and the middle and lower reaches of the West River and the Pearl River estuary. Among the 14 populations, those from Zhaoqing City, Guiping City, and Guangzhou City exhibited relatively high genetic diversity and distinctive genetic characteristics. These findings suggest that the complex hydrological structure and historical connectivity of the Pearl River Basin have contributed to the observed population genetic structure. The genetically diverse populations identified in this study represent valuable wild germplasm resources for the conservation and selective breeding of M. nipponense.
