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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #346198
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Accurate genomic predictions for bacterial cold water disease resistance using low-density SNP panels in rainbow trout

Author
item Vallejo, Roger
item SILVA, RAFAEL - Orise Fellow
item Evenhuis, Jason
item Gao, Guangtu
item Liu, Sixin
item PARSONS, JAMES - Troutlodge, Inc
item MARTIN, KYLE - Troutlodge, Inc
item LOURENCO, DANIELA - University Of Georgia
item Leeds, Timothy - Tim
item Palti, Yniv

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 10/27/2017
Publication Date: 1/16/2018
Citation: Vallejo, R.L., Silva, R., Evenhuis, J., Gao, G., Liu, S., Parsons, J., Martin, K., Lourenco, D., Leeds, T.D., Palti, Y. 2018. Accurate genomic predictions for bacterial cold water disease resistance using low-density SNP panels in rainbow trout [abstract]. World Congress of Genetics Applied in Livestock Production. Species-Aquaculture 2:334.

Interpretive Summary:

Technical Abstract: Previously we have shown accurate genomic predictions for BCWD resistance in rainbow trout using 45K polymorphic SNPs. In this study, we compared the accuracy of genome-enabled breeding values (GEBVs) using 45K, 10K, 3K, 1K, 500, 300, 200 and 70 QTL-flanking SNP panels with the aim of evaluating the effects of low-density SNP panels on the accuracy of predictions in a commercial rainbow trout breeding population. The GEBVs were estimated using the Bayesian variable selection model BayesB, single-step GBLUP (ssGBBLUP) and weighted ssGBLUP (wssGBLUP). The accuracy of GEBVs remained high despite the reductions in SNP density, and even with 500 SNPs it was much higher than the pedigree-based prediction (0.50 - 0.56 vs. 0.36). In addition, the prediction accuracy with the 70 QTL-flanking SNPs (0.65-0.72) was similar to the 45K SNP panel (0.65 - 0.71). We also detected high extent of long-range LD in this population, which likely contributed to the good accuracy of the GEBVs we generated using low-density SNP panels. These results suggest that lower-cost low-density SNP panels can be successfully used for implementing genomic selection for BCWD resistance in rainbow trout aquaculture.