Standardized microsatellite panels for pedigree management of farmed white-leg shrimp (Penaeus vannamei) stocks validated in a VIE tagged family selection line

Abstract

Establishing an effective and reliable system for tracking family pedigree is critical for the success of genetic improvement programs in aquaculture. Parentage assignment using molecular markers can provide an accurate and affordable pedigree management tool for selective breeding projects to maximize genetic gains while minimizing inbreeding levels. In this study, we evaluated 30 microsatellite loci for white-leg shrimp reported in earlier publications and selected 12 markers to develop two standardized multiplex microsatellite panels (SMpv01 and SMpv02) for pedigree management. Mean expected heterozygosity and polymorphic information content across the 12 loci included in the two panels were 0.725 and 0.704 respectively, indicating that the two multiplex panels would be highly informative for parentage assignment analysis. Simulation assignment runs of 10, 000 offspring, originating from 100 candidate dams resulted in complete maternity assignment with more than 11 loci at the 95% confidence level (CI). Capacity of the two marker panels for maternity assignment were tested using CERVUS and COLONY in a family selection line with full sibling relationships inferred from VIE tags. Among 369 individuals from 37 maternal families, CERVUS achieved 100% assignment while 69 assignments could not be matched with pedigree inferred from VIE tags. Overall assignment rate with COLONY was 94.3%, with 29 assignments not consistent with pedigree information from visible implant elastomer (VIE) tags. We also assessed the utility of VIE tags for a combination of nine tag colours and three tagging positions to track family ID via cross validation with molecular assignment. No statistical difference was found for random effects of tag position or VIE tag colour. This indicates that the VIE tag approach tested here would be a highly effective tool for pedigree management of cultured Penaeus vannamei stocks. In summary, our results provide two standardized multiplex microsatellite panels to support pedigree management of farmed white-leg shrimp in a selective breeding program.