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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #335604
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Identification of commercial rainbow trout strains using a SNP panel

Author
item Liu, Sixin
item Palti, Yniv
item MARTIN, KYLE - Troutlodge, Inc
item PARSONS, JAMES - Troutlodge, Inc
item Rexroad, Caird

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/28/2016
Publication Date: 1/13/2017
Citation: Liu, S., Palti, Y., Martin, K.E., Parsons, J.E., Rexroad III, C.E. 2017. Identification of commercial rainbow trout strains using a SNP panel [abstract]. Plant and Animal Genome Conference. P1009.

Interpretive Summary:

Technical Abstract: Assessment of population genetic differentiation is critical for selective breeding of rainbow trout, and identification of fish strains is often required to address production issues arising on fish farms. 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 SNP (single nucleotide polymorphism) panel previously developed for parentage assignment. A total of 1,732 breeders of the eight Troutlodge breeding populations were genotyped with the SNP panel. Both phylogenetic tree and structure analyses revealed that the odd year and even year populations of the same strain were closely related to each other, and 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, 119 fish from two fish farms and 188 fish from four known non-Troutlodge strains. Both egg production fish and farmed fish were correctly assigned to the Troutlodge strain of origin. Furthermore, 185 (98.4%) out of the 188 fish from four non-Troutlodge strains could be excluded as Troutlodge fish. In conclusion, our previously developed SNP panel for parentage assignment is also useful for characterizing genetic differentiation and has sufficient power for genetic assignment of commercial rainbow trout strains used in this study.