Population genetics of Penaeus semisulcatus from Persian Gulf and Oman Sea using newly developed DNA microsatellite markers

A population genetics study on Penaeus semisulcatus from Persian Gulf was performed to assist in the selection of suitable broodstocks for future breeding programs. Eight novel microsatellite loci were developed to study population genetics structure of P. semisulcatus in three population sites, Persian Gulf and Oman Sea (Jask, Hormoz and Kuhestak). There were incidences of heterozygosity deficiency and significant deviations from Hardy Weinberg equilibrium (HWE) at most loci (p<0.001). However, four loci (loci E2 and B9 – Hormoz; loci C6 – Kuhestak; and loci H9 – Jask) found to be in HWE. Micro-Checker analysis revealed null alleles in the three microsatellite loci (B5, C6 and C9). Pairwise Fst comparison based on allelic and genotypic frequencies indicated that the three populations were significantly differentiated from each other (p<0.05). High levels of pairwise Fst (0.106) and low levels of Nm (2.103) observed between Hormoz and Jask populations indicated restricted gene flow between the two populations. On the other hand, low levels of pairwise Fst (0.016) and high levels of Nm (15.876) observed between Hormoz and Kuhestak populations indicated high gene flow between these populations. In this study, the assignment test was examined in order to find gene flow connectivity between the three populations. Overall, results revealed high gene flow between Hormoz and Kuhestak and restricted genetic flow between Jask and both Hormoz and Kuhestak populations, providing new input for selection of genetically-suitable broodstocks.