Pedigree traceability in whiteleg shrimp (Litopenaeus vannamei) using genetic markers: A comparison between microsatellites and SNPs

Abstract

To increase productivity, genetic improvement in cultivated shrimp is of much interest. Evaluation of genetic parameters (e.g., heritability, genotype–environment interaction, inbreeding) and the design of appropriate breeding plans are necessary steps towards genetic improvement. Pedigree traceability by genetic markers is relevant to these objectives. The aim of this study was to compare the performance of 2 genetic marker panels (microsatellites and single nucleotide polymorphisms [SNPs]) for pedigree traceability of a cultivated stock of whiteleg shrimp (Litopenaeus vannamei). Pedigree of a stock from 81 full-sib families reared in a common environment was assessed with microsatellites and SNPs as genetic markers. The panel of 76 SNPs performed better than microsatellites, allowing 94–96% of parentage assignment of the tested progeny (n = 192). A minimum number of 50 SNPs with a proportion of 60% loci with a minimum allele frequency of 0.3 is suitable for successful pedigree assignment. SNP markers are suggested for confidently testing the pedigree of shrimp from known parental broodstock.