SNP discovery in large yellow croaker (Larimichthys crocea) using Roche 454 pyrosequencing sequencing platform

Abstract

Large yellow croaker, one of the most important economic marine fish in China, is mainly distributed in coastal regions of East Asia. Its wild stocks have been collapsed due to overfishing and habitat degradation. However, genetic analysis of the species for population conservation and molecular-aided selection has been largely hindered by insufficient molecular markers. In this study, we used Roche 454 pyrosequencing to develop single nucleotide polymorphism (SNP) markers in large yellow croaker transcriptome. From 4993 transcripts with functional annotation, 5343 putative SNP were detected. Among them, 26 SNPs were randomly selected and 15 loci exhibited significant polymorphisms in genotyping by Sequenom MassARRAY. To our knowledge, this is the first report on the SNP marker development in large yellow croaker based on 454 pyrosequencing RNA sequencing. These SNP could serve as useful marker resources in genetic analysis for population conservation and economic performance improvement of large yellow croaker.