Genomic regions associated with Columnaris disease in two rainbow trout breeding populations

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

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2019
Publication Date: 8/6/2019
Citation: Silva, R., Evenhuis, J., Vallejo, R.L., Gao, G., Martin, K., Leeds, T.D., Lourenco, D., Palti, Y. 2019. Genomic regions associated with Columnaris disease in two rainbow trout breeding populations. Genetics Selection Evolution. 51:42. https://doi.org/10.1186/s12711-019-0484-4.
DOI: https://doi.org/10.1186/s12711-019-0484-4

Interpretive Summary: Using genome-enabled approaches for selective breeding for traits that cannot be measured directly in the potential breeders, like disease resistance, holds a great promise as it provides individual genetic merit estimate for potential breeders compared to family-average estimates in traditional selective breeding. Previously we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. We then evaluated whole-genome enabled selection for BCWD resistance in a commercial rainbow trout population, and found that whole-genome selection can substantially improve the genetic gains in traits that cannot be measured directly on the potential breeders in rainbow trout aquaculture. In the current study we conducted whole genome association analysis and identified chromosome regions harboring genes that affect Columnaris disease (CD) resistance in two important rainbow trout aquaculture populations. Although both populations were found to have similar genetic architecture for this trait and some of the chromosome regions were shared between the two populations, we also detected major differences in the genome location and impact of other regions. Only one of the chromosome regions was found to have an effect on resistance to both BCWD and CD in one of the commercial populations. The results of this study indicate that whole genome selection will be more effective than marker assisted selection approach for CD resistance in rainbow trout. This means that genome-based methods for improved disease resistance will have to be tested and refined for breeding populations that were not included in this study. In addition, the results of this study can be used to further investigate the causative genes affecting CD resistance or susceptibility in rainbow trout, which is important for better understanding of the fish immune system and can lead to further improvement of disease prevention and treatment methods in the aquaculture industry.

Technical Abstract: Columnaris disease (CD) has been identified as an emerging problem for the rainbow trout aquaculture industry in the US. The purpose of this study was to identify genomic regions that explain large portion of the additive genetic variance for CD resistance in rainbow trout (Oncorhynchus mykiss). Two important aquaculture populations were investigated. The National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line, resistant to bacterial cold water disease (BCWD); and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. The number of fish in the pedigree was 54,350 and 36,265, respectively; in which 8,453 and 3,986 fish had phenotypes recorded for CD resistance, 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 14 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 12.45% and 11.17% of the additive genetic variance for CD resistance, respectively. In the TLUM population, a total of 26 windows located on 13 chromosomes were detected. Only four genomic regions with overlapping or neighbouring windows from both populations were detected. The results suggest that CD resistance has an oligogenic architecture in rainbow trout, and the SNP windows found to be associated with CD are not informative enough for selection decisions across populations.