Genetic Diversity and Population Structure of Macrobrachium nipponense in Huaihe River Using Microsatellite Markers

Background: The oriental river prawn (Macrobrachium nipponense) is an economically important aquaculture species in China. Methods: In this study, the genetic diversity and population structure of 12 populations were investigated using ten microsatellite markers. Among them, the Xiaolong Mountain (XLS) population is a cultured stock, while the Songjiachang Reservoir (SJC) population originates from the Yangtze River as an outgroup. Results: A total of 213 alleles were detected across 342 individuals, with an average of 21.3 alleles per locus. The observed heterozygosity (Ho) ranged from 0.362 to 0.902 (mean = 0.724), and the expected heterozygosity (He) ranged from 0.581 to 0.925 (mean = 0.805). Shannon’s diversity index (I) ranged from 1.224 to 2.810 (mean = 2.130). The polymorphism information content (PIC) varied from 0.532 to 0.920 (mean = 0.787), indicating high informativeness of the markers. Population structure analysis revealed a weak genetic subdivision with a subtle clustering signal (K = 2), but evaluation of LnP(K) indicated that K = 1 could not be confidently rejected. Pairwise Fst values ranged from 0.008 to 0.058, with high gene flow (Nm = 4.060–31.000), denoting low-to-moderate genetic differentiation. AMOVA showed that 98% of genetic variation resided within populations, with only 2% among populations (overall Fst = 0.020, p < 0.01). Nei’s genetic distances ranged from 0.094 to 0.277. Conclusions: Overall, the 12 populations of M. nipponense exhibited high genetic diversity, low-to-moderate genetic differentiation, and a weak population structure with most variation residing within populations. These findings provide valuable molecular markers for selective breeding and offer theoretical guidance for the conservation and sustainable utilization of M. nipponense germplasm resources, although the inferred population structure should be interpreted with caution given the weak differentiation signal.