SSR-EST and SNP-EST genomic annotation and population validation for candidate genes identification in marine shrimp Litopenaeus vannamei (Penaeidae, Decapoda)

Abstract

Litopenaeus vannamei is known as Pacific white shrimp, the main penaeid marketed worldwide. Despite its excellent performance in captivity, there is a concern to properly manage the herds, due to the absence of introduction of a new gene pool, resulting in increased inbreeding and decreased levels of genetic diversity. In this context, molecular markers contained in expressed regions of the genome (EST, Expressed Sequence Tags), such as microsatellite or SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphisms), are useful in accessing stocks genetic variation, identification of loci linked to traits of interest and establishment of breeding programs based on Marker Assisted Selection (MAS). The development of the L.vannamei EST Genome Project(ShEST) allowed the characterization of thousands of SSR and SNP, and most of these markers were not evaluated in populations nor elucidated with its gene product yet. Thus, this work aims to describe the gene products of EST-SSR and EST-SNP loci and their possible pathways, as well as validation in superior stocks for growth and pathogen resistance. Based on the gene products from genome annotation, some of these loci, contained in genes of interest, will be selected for verification of a possible association with economically important traits. The breeding and measurement of performance characteristics will be conducted by Aquatec and Genearch Ltda Companies (RN, Brazil). The analysis of association between genotypes and phenotypes observed may provide a set of informative markers to assist an efficient management and monitoring of stocks of this species in Brazil.