Genome-wide mapping of quantitative trait loci that can be used in marker-assisted selection for resistance to bacterial cold water disease in two commercial rainbow trout breeding populations

Authors: Vallejo, Roger; Evenhuis, Jason; CHENG, HAO - University Of California, Davis; FRAGOMENI, BRENO - University Of Connecticut; Gao, Guangtu; Liu, Sixin; Long, Roseanna; Shewbridge, Kristy; SILVA, RAFAEL M. - Zoetis; Wiens, Gregory - Greg; Leeds, Timothy - Tim; MARTIN, KYLE - Troutlodge, Inc; Palti, Yniv

Submitted to: Aquaculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2022
Publication Date: 11/15/2022
Citation: Vallejo, R.L., Evenhuis, J., Cheng, H., Fragomeni, B.O., Gao, G., Liu, S., Long, R., Shewbridge, K., Silva, R.O., Wiens, G.D., Leeds, T.D., Martin, K.E., Palti, Y. 2022. Genome-wide mapping of quantitative trait loci that can be used in marker-assisted selection for resistance to bacterial cold water disease in two commercial rainbow trout breeding populations. Aquaculture. 560(738574). https://doi.org/10.1016/j.aquaculture.2022.738574.
DOI: https://doi.org/10.1016/j.aquaculture.2022.738574

Interpretive Summary: Bacterial cold water disease (BCWD) causes significant mortality and economic losses in rainbow trout aquaculture. The main goal of our research is to improve genetic resistance against this disease using state-of-the-art genome-wide association analyses and genomic selection approaches that improve the accuracy of genetic merit predictions in commercial breeding populations. Commercial rainbow trout breeding is complicated by multiple populations that spawn naturally at different times of the year and often multiple year-classes are maintained. Previously, we found that resistance to BCWD was controlled by five to six chromosome regions that harbor genes with moderate to large effect on disease resistance in a single commercial population. In the current study, we conducted genome-wide association analysis using rainbow trout from an additional commercial population that was originated from the same source population. Our results confirmed that resistance to BCWD is controlled by five to nine chromosome regions with moderate to large effects on disease resistance in the two populations. While the chromosome region with largest effect was shared between the two populations, other moderate-large effect chromosome regions were not shared by the two populations. This result shows that it is important to conduct new genomic analysis in each population to validate the results from previous studies as differences in the genetic architecture of disease resistance can exist even between populations originating from the same source.

Technical Abstract: Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is a frequent and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. A focus of our research is to improve genetic resistance against this disease in commercial populations. Commercial rainbow trout breeding is complicated by multiple populations that spawn naturally at different times of the year and often multiple year-classes are maintained. Previously, we found that resistance to BCWD in the 2013 year-class (YC) of the Troutlodge May spawning breeding population was controlled by oligogenic inheritance of five to six moderate to large effect QTL and many small effect loci. In the current study we performed genome-wide association analyses using rainbow trout from YC 2015 and YC 2016 that were separated as two closed breeding populations for seven generations. Our results confirmed that resistance to BCWD in the even-year population (YC 2016) is also controlled by oligogenic inheritance of nine QTLs with moderate-large effects that individually explained 2.1% - 34.7% of the additive genetic variance. The nine QTL regions detected in YC 2016 jointly explained up to 88% of the additive genetic variance and the five detected QTLs in YC 2015 jointly explained up to 61% of the genetic variance. The largest effect and most significant QTL is shared between the two YC populations on chromosome Omy25. This QTL was previously shown to be useful for marker-assisted selection (MAS) in the odd-year may spawning population and it should also be the best candidate for MAS in the even-year population. On the other hand, two other moderate-large effect QTL were not shared by the two YC populations, demonstrating that differences in the trait genetic architecture can exist between populations that were originated from the same source due to founders’ effect and genetic drift in small populations.