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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #369897

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Identification of additional single nucleotide polymorphisms associated with resistance to bacterial cold water disease in rainbow trout using whole genome resequencing

Author
item Liu, Sixin
item Gao, Guangtu
item Long, Roseanna
item Evenhuis, Jason
item Wiens, Gregory - Greg
item MARTIN, KYLE - TROUTLODGE, INC.
item Palti, Yniv

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2019
Publication Date: 1/10/2020
Citation: Liu, S., Gao, G., Long, R., Evenhuis, J., Wiens, G.D., Martin, K.E., Palti, Y. 2020. Identification of additional single nucleotide polymorphisms associated with resistance to bacterial cold water disease in rainbow trout using whole genome resequencing. Plant and Animal Genome Conference. P.NO.W065.

Interpretive Summary:

Technical Abstract: Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is a major disease in rainbow trout (Oncorhynchus mykiss). Previously, we have reported two major QTL associated with BCWD resistance on chromosomes Omy8 and Omy25. The objectives of this study were to identify additional single nucleotide polymorphisms (SNPs) associated with resistance to BCWD using whole genome resequencing, and to identify candidate genes for BCWD resistance. We conducted two rounds of pool-seq analysis in the Troutlodge odd-year May spawning population. For the first round of pool-seq, we pooled the DNA of parents based on their QTL haplotypes and the BCWD survival phenotypes of their offspring. In the second round of pool-seq, we pooled parental DNA samples solely based on BCWD phenotypes to avoid bias due to haplotype pre-selection. Over 10 million SNPs were identified in each round of pool-seq. Based on the first round of pool-seq, new SNPs showing significantly different allele frequencies between the two pools were used to genotype the 2015 Troutlodge May spawning population, and 26 SNPs associated with the BCWD resistance were validated. Candidate genes for the Omy08 QTL have also been identified after examining the functional annotation of the validated SNPs. Based on the second round of pool-seq, additional SNPs potentially associated with the two BCWD QTL have been identified, and we are currently evaluating those SNPs using the 2015 Troutlodge May spawning population.