Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia

The purpose of current study is to illustrate the utility of EST-derived SSR in characterizing wild populations of Macrobrachium rosenbergii in Malaysia‘s rivers. A novel set of EST-SSR was validated in a full panel of 120 samples from four wild populations through Polymerase Chain Reaction (PCR). Seven EST-SSR loci were identified, characterized, and evaluated on 30 individuals each from the populations namely Sg. Tapah (Perak), Sg. Timun (Negeri Sembilan), Sg. Bernam (Selangor) and Sg. Johor (Johor). The average polymorphic informative content value (PIC) for these seven primers was found to be 0.5355 indicating considerable degree of polymorphism with number of alleles detected ranged from 5 to 17. The observed heterozygosity value count during multi-population analyses ranged from 0.3668 to 0.4554, whilst the expected ranged from 0.5192 to 0.5700. There was linkage disequilibrium (LD) observed between 2 pairs of EST-SSRs loci. All loci have deviation from the Hardy-Weinberg equilibrium (HWE) except EST-Mr-AS-31957, suggesting factors violating the neutral expectation such as selection and non random mating. The FIS index demonstrated indication of inbreeding among individuals of each population. There was evidence that all samples from four sampling sites assessed in this study are drawn from four clusters (k=4). Estimate of fixation index value in pairwise comparisons among the four localities revealed very low magnitude of differentiation (R ST ranged between 0.0000 to the highest of 0.17918). The findings of this study suggested that intra-specific diversity that occurs between studied populations were not extremely high, as very low variation was detected in pairwise comparisons and genetic structuring analyses. The ongoing gene flow either naturally or via translocations by humans are possible reasons for the low magnitude of genetic differentiation. The overall results suggest that all populations (Tapah, Timun, Bernam, and Johor) were composed of one large possible panmictic population for management purposes at present. Also the results indicated that these polymorphic EST-SSR derived from M. rosenbergii would be useful for population genetic structure analysis and genetic diversity assessment in prawn populations as part of management policies of natural resources to ensure sustainability of wild broodstock for future development of prawn culture industries.

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