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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #347669
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population

Author
item Palti, Yniv
item Liu, Sixin
item Vallejo, Roger
item MARTIN, KYLE - Troutlodge, Inc
item Evenhuis, Jason
item Gao, Guangtu
item Wiens, Gregory - Greg
item Leeds, Timothy - Tim

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2017
Publication Date: 1/13/2018
Citation: Palti, Y., Liu, S., Vallejo, R.L., Martin, K., Evenhuis, J., Gao, G., Wiens, G.D., Leeds, T.D. 2018. Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population. Plant and Animal Genome Conference. International Plant and Animal Genome XXVI. Paper No. 103.

Interpretive Summary:

Technical Abstract: Previously we have demonstrated that genomic selection (GS) for bacterial cold water disease (BCWD) resistance can double the accuracy of traditional pedigree-based selection in a commercial rainbow trout breeding population. The objective of this study was to evaluate the effectiveness of marker assisted selection (MAS). Application of MAS is more economical than GS as genotyping fewer SNPs has less cost. In addition, SNP haplotypes that are in tight linkage disequilibrium with the favorable QTL alleles can be used for direct selection of breeding animals eliminating the need for re-phenotyping and re-training of the GS or P-BLUP models in every generation. Here, we have confirmed that the favorable SNP haplotypes from three major QTL we have identified in the May 2013 nucleus breeding population of Troutlodge, Inc. were still strongly associated with improved BCWD resistance in the following May 2015 generation. Furthermore, using progeny testing data we have found that the combined predictive ability, or accuracy, of the favorable QTL haplotypes was consistent across two generations, and substantially better than the accuracy of the pedigree based BLUP predictions of genetic merit. Overall, our results indicate that MAS using a combination of favorable haplotypes from few large-effect QTL regions can rapidly and accurately identify elite candidate breeders for BCWD resistance in a commercial rainbow trout breeding population.