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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #338863
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Genome-wide association studies identify 25 genetic loci associated with resistance to Bacterial Cold Water Disease in rainbow trout

Author
item Vallejo, Roger
item Liu, Sixin
item Gao, Guangtu
item FRAGOMENI, BRENO - University Of Georgia
item HERNANDEZ, ALVARO - University Of Illinois
item Leeds, Timothy - Tim
item PARSONS, JAMES - Troutlodge, Inc
item MARTIN, KYLE - Troutlodge, Inc
item Evenhuis, Jason
item Welch, Timothy - Tim
item Wiens, Gregory - Greg
item Palti, Yniv

Submitted to: Gordon Research Conferences
Publication Type: Abstract Only
Publication Acceptance Date: 2/26/2017
Publication Date: 2/28/2017
Citation: Vallejo, R.L., Liu, S., Gao, G., Fragomeni, B.O., Hernandez, A.G., Leeds, T.D., Parsons, J., Martin, K., Evenhuis, J., Welch, T.J., Wiens, G.D., Palti, Y. 2017. Genome-wide association studies identify 25 genetic loci associated with resistance to Bacterial Cold Water Disease in rainbow trout [abstract]. Gordon Research Conferences. P245.

Interpretive Summary:

Technical Abstract: Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonids aquaculture. In previous studies we have identified moderate-large effect QTL for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a high density SNP array and linkage map have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we identified 25 moderate-large effect QTL associated with BCWD resistance in two different rainbow trout breeding populations using two genotyping platforms, the 57K Affymetrix SNP array and restriction-associated DNA (RAD) SNP genotyping, coupled with dense multipoint genetic maps and multiple-regression GWAS models. Nine of the detected QTL were segregating in both NCCCWA and TLUM rainbow trout populations which explained a significant proportion of host genetic variation in resistance to BCWD in both populations (~44%), suggesting a common underlying genetic architecture of BCWD resistance across the tested populations. These results confirmed that BCWD resistance in rainbow trout is primarily controlled by the oligogenic inheritance of few moderate-large effect loci and many minute effect polygenic loci. We compared two GWAS algorithms and the GWAS with weighted single-step GBLUP detected higher number of QTL than the BayesB algorithm. The RAD-SNPs, which were only used in the NCCCWA population, detected higher number of QTL than the 57K SNP array. This suggests that despite their lower marker density (24K SNP), RAD SNPs uncover polymorphisms that are more unique and informative for the specific population in which they are discovered. The QTL information we identified in this study will be analyzed for presence of positional candidate genes and will also be evaluated for improving the efficiency of genome-enabled selection schemes for BCWD resistance in rainbow trout aquaculture.