Rainbow trout (Onchorhynchus mykiss) is one of the most important freshwater aquaculture fish in Iran. It is necessary to development available molecular marker associated with genetic variation in maturation for O. mykiss. In this study, 52 novel SNP markers for O. mykiss were discovered for functional markers, and validated based on transcriptome sequencing with the Illumina Hiseq2500 platform and most of variants cause synonymous mutations in protein . The observed and expected heterozygosities ranged from 0.177 to 1.000 and 0.239 to 0.638 , respectively. The minimum allele frequency (MAF) ranged from 0.166 to 0.489. Among these SNP loci, twenty two loci showed significant departures from the Hardy–Weinberg equilibrium after Bonferroni correction ( p < 0.05) and significant linkage disequilibrium was found. These data provide valuable transcript sequence and functional marker resources for the quantitative trait locus (QTL) identification. The SNP markers would be used in genetic studies helping economic performance improvement and management of this species.
Keywords: Single nucleotide polymorphism (SNP); Rainbow trout; Next generation sequencing; RNA-seq