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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #359060
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Whole genome resequencing refines genomic regions associated with bacterial cold water disease resistance in rainbow trout

Author
item Liu, Sixin
item Gao, Guangtu
item Wiens, Gregory - Greg
item Palti, Yniv

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/29/2018
Publication Date: 1/12/2019
Citation: Liu, S., Gao, G., Wiens, G.D., Palti, Y. 2019. Whole genome resequencing refines genomic regions associated with bacterial cold water disease resistance in rainbow trout. [abstract]. Plant and Animal Genome Conference. p. PE0262.

Interpretive Summary: 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 objective of this study was to refine the genomic regions associated with BCWD resistance using whole genome resequencing. Two filtering steps were used to select parents of phenotyped offspring from two generations of the Troulodge May Spawning nucleus population for sequencing. First, the families in each generation were sorted by BCWD survival rates. The parents of the top 20 families were assigned to a resistant group (R), and the parents of the bottom 20 families were assigned to a susceptible group (S). Then, the haplotypes in the two QTL regions were reconstructed in each parent using the genotypes from our previous study. Ten R parents homozygous for the favorable Omy8 haplotype and ten S parents without the favorable Omy8 haplotype were selected for sequencing in the 2015 generation. Similarly, ten R parents homozygous for the favorable Omy25 haplotype and ten S parents without the favorable Omy25 haplotype were selected for sequencing in the 2017 generation. Over 15 million SNPs were identified from resequencing in this population and the two major QTL were narrowed down to regions much smaller than those reported previously. We are currently examining the reference genome sequence to identify candidate genes for BCWD resistance within the narrowed QTL regions.

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 objective of this study was to refine the genomic regions associated with BCWD resistance using whole genome resequencing. Two filtering steps were used to select parents of phenotyped offspring from two generations of the Troulodge May Spawning nucleus population for sequencing. First, the families in each generation were sorted by BCWD survival rates. The parents of the top 20 families were assigned to a resistant group (R), and the parents of the bottom 20 families were assigned to a susceptible group (S). Then, the haplotypes in the two QTL regions were reconstructed in each parent using the genotypes from our previous study. Ten R parents homozygous for the favorable Omy8 haplotype and ten S parents without the favorable Omy8 haplotype were selected for sequencing in the 2015 generation. Similarly, ten R parents homozygous for the favorable Omy25 haplotype and ten S parents without the favorable Omy25 haplotype were selected for sequencing in the 2017 generation. Over 15 million SNPs were identified from resequencing in this population and the two major QTL were narrowed down to regions much smaller than those reported previously. We are currently examining the reference genome sequence to identify candidate genes for BCWD resistance within the narrowed QTL regions.