Genetic diversity and differentiation of cultured Macrobrachium rosenbergii in China using newly developed microsatellite multiplex PCR panels.

The giant freshwater prawn, Macrobrachium rosenbergii, is one of the most crucial crustacean species cultured in China. However, in recent years, M. rosenbergii aquaculture in China has encountered several challenges, including low productivity and growth retardation. A decline in genetic variation has been implicated in this phenomenon. This study aims to develop microsatellite multiplex PCR panels to elucidate the genetic diversity and differentiation of cultured M. rosenbergii populations in China. Based on our previous transcriptome sequencing, we developed 24 polymorphic molecular markers. The average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were 4.042, 0.535, 0.605, and 0.543, respectively. Two multiplex PCR panels involving six microsatellite loci were obtained by combining different amplicon lengths from these 24 loci. The panels were used to evaluate the genetic structure of six cultured M. rosenbergii populations in China, including one population in Guangxi (GX) and another in Guangdong (GD) province, along with two populations each in Jiangsu (JSA and JSB) and Zhejiang (ZJA and ZJB) provinces. Results revealed that the polymorphism among the six populations ranged from 0.365 to 0.682 with reduced genetic diversity in ZJA and JSB populations (PIC < 0.5). Pairwise FST, Nei's genetic distance, and STRUCTURE analysis revealed significant differentiation among the six cultured populations. ZJA and GD exhibited pronounced genetic distinctiveness from the other populations and were consequently assigned to distinct groups. Populations GX and JSB (FST=0.058, DA=0.045) and populations ZJB and JSA (FST=0.009, DA=0.016) were assigned to two clusters, respectively, suggesting they share similar origins. This study provided polymorphic microsatellite markers and genetic diversity assessment of cultured M. rosenbergii populations, laying a foundation for future breeding programs. [ABSTRACT FROM AUTHOR]