RNA-Seq Identifies SNPs Associated with Muscle growth and Quality in Rainbow Trout

Rainbow trout (Oncorhynchus mykiss) is one of the top five sport fish species in North America and the second most widely cultivated fish species for food. Quality attributes of fish flesh are important determinants of profitability for the food fish aquaculture industry. Single nucleotide polymorphism (SNP) determines 90% of human genetic variations. Our previous RNA-Seq studies were successful in finding SNP markers associated with growth traits in rainbow trout. In this study, RNA-Seq was used to identify SNPs associated with some important quality attributes of fish flesh including muscle yield, fat content, flesh color and shear force. Total RNA was isolated from four families (5 fish per family), ranked high and low for these traits, and RNA was sequenced using an illumina platform. Sequencing reads from contrasting families were mapped to the reference genome/transcriptome to predict SNPs associated with each quality attribute. Phenotypic variations in these quality traits were measured in 100 families from two generations from the USDA/NCCCWA rainbow trout breeding program. Predicted SNPs were validated by the Sequenom genotyping technique. Out of validated SNPs, 42 SNPs were evaluated for association with aforementioned traits in approximately 1000 fish from two generations. The study identified SNPs (potential genetic markers) associated with these quality attributes. A limited number of differentially regulated genes were identified that are associated with each quality attribute, perhaps, indicating that selective breeding have had a relatively low impact on modifying gene expression.