Submitted to: Aquaculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2016
Publication Date: 10/5/2016
Citation: Liu, S., Palti, Y., Martin, K.E., Parsons, J.E., Rexroad, III, C.E. 2016. Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel. Aquaculture. 468(1):120-125. doi: 10.1016/j.aquaculture.2016.10.004.

Interpretive Summary: Rainbow trout is the most widely cultured cold freshwater fish in the world, with production on every continent except Antarctica. Troutlodge, Inc., one of the largest commercial rainbow trout egg producers in the world, has developed four strains (February, May, August and November) of rainbow trout with distinct spawning times. Each strain has two year-class breeding populations (even year and odd year). Thus, a total of eight breeding populations are maintained in the Troutlodge breeding program. Previously, we developed a marker panel to reconstruct fish pedigree. In this study, we demonstrate that the marker panel is also useful to evaluate the genetic relationships among the eight breeding populations and has sufficient power to determine whether fish sampled from the farm have orginatd from one of the four Troutlodge breeding strains.

Technical Abstract: Rainbow trout (Oncorhynchus mykiss) is the most widely cultured cold freshwater fish in the world, with production on every continent except Antarctica. Troutlodge, Inc., one of the largest commercial rainbow trout egg producers in the world, has developed four strains (February, May, August and November) of rainbow trout with distinct spawning times. Each strain has two year-class breeding populations (even year and odd year). Thus, a total of eight breeding populations are maintained in the Troutlodge breeding program. Previously, we developed and validated a SNP (single nucleotide polymorphism) panel which was optimized 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 1,732 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. One group included the populations of February and May strains and the other group included the populations of August and November strains. 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 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.