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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #346446
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Prospecting genomic regions associated with columnaris disease in two rainbow trout breeding populations

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

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 10/19/2017
Publication Date: 2/16/2018
Citation: Silva, R., Evenhuis, J., Vallejo, R.L., Gao, G., Martin, K., Leeds, T.D., Lourenco, D., Palti, Y. 2018. Prospecting genomic regions associated with columnaris disease in two rainbow trout breeding populations [abstract]. World Congress of Genetics Applied in Livestock Production. GP2.

Interpretive Summary:

Technical Abstract: Flavobacterium Columnare, the causative agent of Columnaris disease (CD), is distributed around the world in fresh water sources, infecting freshwater finfish species. Recently it has been identified as an emerging problem for the rainbow trout aquaculture industry in the US. The purpose of this study was to prospect genomic regions that explain large portion of the additive genetic variance of CD resistance in rainbow trout. Two important aquaculture populations were investigated. The National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line, with resistance to bacterial cold water disease (BCWD); and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population, which provided 54,350 and 36,265 pedigree records; in which 8,453 and 3,986 fish had CD resistance phenotype records, respectively. Fish that survived to 21 days post immersion challenge were recorded as resistant. Genotypes for 57k SNP (Affymetrix Axiom®) were available for 1,185 and 1,137 fish from NCCCWA and TLUM, respectively. The SNP effects and variances were estimated using the weighted single-step genomic BLUP approach for genome-wide association (WssGBLUP), which uses pedigree, genotypes, and phenotypes from genotyped and ungenotyped animals. The weighting strategy accounted for 1Mb moving SNP-windows along each of the 29 chromosomes in the reference genome. Genomic regions that explained more than 1% of the additive genetic variance were considered associated with CD resistance. A total of 13 windows located on six chromosomes were found to be associated with CD resistance in the NCCCWA population. Two windows, located at 59-60 Mb and 61-62 Mb on chromosome Omy17, explained 12% and 11.33% of the genetic variance for CD resistance, respectively. In the TLUM population, a total of 16 windows located on nine chromosomes were detected. Only three similar windows (located on two chromosomes) were detected in both populations. The results suggest that CD resistance has an oligogenic architecture, and the SNP windows found to be associated with CD are not informative enough for selection decisions across populations.