Isolation and characterization of SNP markers of rainbow trout (Onchorhynchus mykiss Walbaum, 1792) from transcriptomic sequences.

Rainbow trout (Onchorhynchus mykiss) is one of the most important freshwater aquaculture fish in Iran. It is necessary to develop available molecular marker such as SNPs, which represent a useful tool in detecting adaptive signals in populations and also parentage assignment for O. mykiss. Genetic architecture of broodstock populations is important for breeding programs, as it enables decisions on broodstock screening and genomic selection. In this study, 52 novel single nucleotide polymorphism (SNP) markers for O. mykiss were discovered and validated based on transcriptome sequencing, by means of paired-end sequencing in an Illumina HiSeq 2500 platform. The SNPs were identified through liver transcriptome sequencing from fifteen samples. 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. The SNP markers identified in this research could be useful for novel studies, such as those related to associations between high-resolution molecular markers and quantitative traits studies. Moreover, these SNP markers would be used in genetic studies helping economic performance improvement and management of this species.