Genetic diversity in farmed and wild populations of the giant freshwater prawn (Macrobrachium rosenbergii)based on microsatellite DNA marker analysis

Abstract

Macrobrachium rosenbergii is one of the most important aquaculture species in Bangladesh. Understanding a population’s ge-netic structure is vital for developing effective conservation strategies, allowing population monitoring, and identifying vulnerable groups. This study assessed genetic diversity in two hatchery populations (Fish-Tech prawn hatchery and CP prawn hatchery) and two wild populations (Indurkani point of Kocha River-2022 and Zianagar point of Kocha River-2023) of M. rosenbergii using microsatellite DNA markers. Nine microsatellite loci were analyzed, and all were found to be polymorphic across the populations. The number of alleles (N a ) per locus ranged from 3 to 11. The mean N a in the Fish-Tech, CP, and Kocha River samples was 6.000, 6.778, and 7.055, respectively. The observed heterozygosity (H o ) was lower than the expected heterozygosity (He) in all four populations. Polymorphism information content (PIC) values ranged from 0.335 to 0.887 across four populations, indicating moderate to high marker effectiveness. Significant deviations from Hardy–Weinberg expectations were observed in 35 of 36 tests. The population differentiation (F ST ) values indicate a moderate genetic differentiation among the populations. The analysis of molecular variance (AMOVA) revealed that only 10% of the variance exists among populations. Complying with the neighbor-joining tree and principal coordinate analysis (PCoA), and STRUCTURE analysis revealed two distinct clusters; two samples of the Kocha River comprise one cluster, and the two hatchery samples comprise another cluster. These findings provide a baseline for future breeding program development and genetic monitoring.