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 polymorphisms) associated with BCWD resistance in rainbow trout. The objectives of this study were (1) to validate the SNPs associated with BCWD resistance in a commercial 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 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 from each of the 138 full-sib families of the 2015 generation, and 37 SNPs associated with BCWD resistance were validated. Thirty-six of the validated SNPs were clustered on chromosomes Omy3, Omy8 and Omy25. Thus, at least three QTL (quantitative trait loci) for BCWD resistance were validated in the 2015 generation. Three SNPs from each QTL region were used for haplotype association analysis. Three haplotypes, Omy3TGG, Omy8GCG and Omy25CGG, were found to be associated with BCWD resistance in the 2015 generation. 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 positively 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, which was equal or greater 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.
Highlights
Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is one of the most devastating diseases in rainbow trout (Oncorhynchus mykiss) aquaculture (Nematollahi et al, 2003; Starliper, 2011; Loch and Faisal, 2015)
For each QTL region, we identified one haplotype associated with BCWD resistance and one haplotype associated with BCWD susceptibility
The haplotypes of each parent were reconstructed for each QTL region, and we evaluated retrospectively the accuracies of marker-assisted selection (MAS) for BCWD resistance using the favorable haplotype for each QTL region (Table 5, Figure S1)
Summary
Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is one of the most devastating diseases in rainbow trout (Oncorhynchus mykiss) aquaculture (Nematollahi et al, 2003; Starliper, 2011; Loch and Faisal, 2015). Use of licensed antibiotics for BCWD treatment increases production costs, and antibioticresistant pathogens may emerge. Genetic variation for BCWD resistance (Hadidi et al, 2008; Silverstein et al, 2009) has been documented in rainbow trout. A rainbow trout line with improved BCWD resistance has been developed (Leeds et al, 2010; Wiens et al, 2013a). Family-based selection is based on the family breeding values estimated from pedigree relationships and BCWD phenotypes. Evaluation for BCWD resistance in rainbow trout is labor intensive and time consuming. Familybased selection cannot exploit within-family genetic variation because disease challenged individuals are excluded as selection candidates, and selection is based on family means obtained from the BCWD performance of siblings of the selection candidates. Selection methods that can utilize within-family variation at an affordable cost are desirable
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