Genetic diversity and population structure of wild and domesticated black tiger shrimp (Penaeus monodon) broodstocks in the Indo-Pacific regions using consolidated mtDNA and microsatellite markers

Abstract

Black tiger shrimp (Penaeus monodon) is one of the most important internationally traded fishery species, and the commercial success of their aquafarming primarily depends on the high quality broodstock for seed production. Therefore, identifications of genetically diverse broodstocks of P. monodon are essential to eliminate inbreeding effects, ensure sustainable seed supply, and facilitate genetic upgrading for selective breeding and restocking programs. The present study used a combination of mtDNA control region sequences and ten microsatellite markers to evaluate the genetic diversity, demographic history and population structure of P. monodon broodstocks collected from five sampling locations across the Indo-Pacific regions. The domesticated P. monodon broodstock populations were collected from Hawaii, USA (MMO), Thailand (MT) and Madagascar (MD), while the wild broodstock populations were collected from Japan (MJ) and Malaysia (MS). Clustering analyses based on the Principle Component Analysis (PCA), Canonical Variate Analysis (CVA), STRUCTURE, and Neighbour-Joining (NJ) phylogenetic analysis revealed that the domesticated populations were unequivocally diverged from the wild-caught populations. Haplotype networks, neutrality testing, and mismatch distribution analysis indicated a complex population expansion pattern involving Wahlund effect based on human translocation, and continental drift during the paleogeographic event in Pleistocene glacial age. Both mtDNA and microsatellite data detected relatively high levels of genetic diversity among all populations, but higher levels of nucleotide diversity in the wild populations, given that the artificial selection in aquaculture practice could reduce the genetic heterogeneity of the domesticated populations. The negative correlation of isolation by distance (IBD) results further supported the findings from neutrality test, indicating that founder stocks for genetic improvement program which were established from several geographic origins may have caused admixture in the domesticated populations. The genetic information obtained from this study could help to establish appropriate breeding strategies and genetic improvement program, and would provide essential data for genetic management and conservation of P. monodon wild populations.