Evaluation of marker-assisted selection for resistance to bacterial cold water disease in three generations of a commercial rainbow trout breeding population

Authors: Liu, Sixin; Vallejo, Roger; Evenhuis, Jason; MARTIN, KYLE - Troutlodge, Inc; HAMILTON, ALASTAIR - Hendrix Genetics; Gao, Guangtu; Leeds, Timothy - Tim; Wiens, Gregory - Greg; Palti, Yniv

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2018
Publication Date: 8/3/2018
Citation: Liu, S., Vallejo, R.L., Evenhuis, J., Martin, K.E., Hamilton, A., Gao, G., Leeds, T.D., Wiens, G.D., Palti, Y. 2018. Evaluation of marker-assisted selection for resistance to bacterial cold water disease in three generations of a commercial rainbow trout breeding population [serial online]. Frontiers in Genetics. 9:286. https://doi.org/10.3389/fgene.2018.00286.
DOI: https://doi.org/10.3389/fgene.2018.00286

Interpretive Summary: Bacterial cold water disease (BCWD) causes significant mortality and economic losses in rainbow trout aquaculture. Traditional breeding for BCWD resistance requires extensive disease challenge experiments to identify families with BCWD resistance, which is time consuming and labor intensive. Previously, we have identified genetic markers associated with BCWD resistance in rainbow trout. In this study, we validated the genetic markers for BCWD resistance in a commercial rainbow trout breeding population, and demonstrated that the genetic markers can be used to select fish with BCWD resistance in three generations of this commercial breeding population. The selection accuracy of this method is equal or even better than that of traditional breeding in the same generation. Thus, the method reported in this study provides an alternative approach to select fish with BCWD resistance.

Technical Abstract: Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is an endemic and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. Previously, we have identified SNPs (single nucleotide polymorphism) associated with BCWD resistance in rainbow trout. The objectives of this study were 1) to validate the SNPs associated BCWD resistance in a commercial Troutlodge breeding population; and 2) to evaluate retrospectively the accuracy of MAS (marker-assisted selection) for BCWD resistance in this commercial breeding program. Three consecutive generations, 2013TLUM, 2015TLUM and 2017TLUM, of the Troutlodge May breeding population were evaluated for BCWD resistance. Based on our previous studies, a panel of 96 SNPs was selected and used to genotype the parents and ten offspring of each138 full-sib families of the 2015TLUM generation, and 37 SNPs associated with BCWD resistance were validated. All validated SNPs, except one, were clustered on chromosomes Omy3, Omy8 and Omy25. Thus, at least three QTL (quantitative trait loci) for BCWD resistance were validated in the 2015TLUM generation. Three SNPs from each QTL region were used for haplotype association analysis, and three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, associated with BCWD resistance in the 2015TLUM generation were identified. Retrospective analyses were then performed to evaluate the accuracy of MAS for BCWD resistance using these three favorable haplotypes. The accuracy of MAS was estimated with the Pearson correlation coefficient between the total number of favorable haplotypes in the two parents and the family BCWD survival rates. The Omy8 and Omy25 haplotypes were consistently correlated with the family BCWD survival rates across all three generations. The accuracies of MAS using these two haplotypes together were consistently around 0.5 across all three generations, which was equal or even higher than the accuracy of the conventional family-based selection in the same generation. In conclusion, we have demonstrated that MAS for BCWD resistance is feasible in this commercial rainbow trout breeding population.