Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel

Rainbow trout (Oncorhynchus mykiss) is the most widely cultured cold freshwater fish in the world. Troutlodge, Inc., one of the largest commercial rainbow trout egg producers in the world, has eight breeding populations of rainbow trout. Assessment of population genetic differentiation is critical for selective breeding, and genetic assignment is often required to address production issues arising on fish farms. Previously, we developed a SNP (single nucleotide polymorphism) panel for parentage assignment in rainbow trout. The objectives of this study were: (1) to characterize the genetic differentiation of the eight Troutlodge breeding populations; and (2) to evaluate the accuracy of genetic assignment to identify Troutlodge fish using the same SNP panel previously developed for parentage assignment. A total of 1732 breeders of the eight Troutlodge breeding populations were genotyped with the SNP panel. The global FST over all SNPs was 0.13 and the pairwise FST between any two breeding populations ranged from 0.056 to 0.195. Both phylogenetic tree and structure analyses revealed that the odd year and even year populations for the same strain were closely related to each other. Also, the eight populations were clustered into two groups. Based on the results of self-assignment, 97.1% of the Troutlodge breeders were correctly assigned to the population of origin. To further evaluate the accuracy of genetic assignment, we also genotyped 280 egg production fish from three Troutlodge populations of known origin, 49 fish from a Canadian farm, 70 fish from a farm in Idaho and 188 fish from four known non-Troutlodge strains. Among the 280 production fish, 98.2% fish were correctly assigned to the Troutlodge strain of origin. Consistent with the purchasing records, the fish from the two farms were also correctly assigned to two Troutlodge strains. Based on the SNP genotypes, 185 out of 188 fish (98.4%) from the four non-Troutlodge strains could be excluded as Troutlodge fish. In conclusion, our previously developed SNP panel for parentage assignment is also useful to characterize genetic differentiation and has sufficient power for genetic assignment of commercial rainbow trout strains used in this study.