Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population

Authors: Vallejo, Roger; CHENG, HAO - University Of California, Davis; FRAGOMENI, BRENO - University Of Connecticut; Shewbridge, Kristy; Gao, Guangtu; MACMILLAN, JOHN - Clear Springs Foods, Inc; TOWNER, RICHARD - Gentec Consulting; Palti, Yniv

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2019
Publication Date: 8/29/2019
Citation: Vallejo, R.L., Cheng, H., Fragomeni, B.O., Shewbridge, K., Gao, G., Macmillan, J.R., Towner, R., Palti, Y. 2019. Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population pserial online]. Genetic Selection Evolution. 51:47. https://doi.org/10.1186/s12711-019-0489-z.
DOI: https://doi.org/10.1186/s12711-019-0489-z

Interpretive Summary: Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods (CSF), Inc. has been applying traditional pedigree-based selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. 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 evaluated whole-genome enabled selection for bacterial cold-water disease resistance in another commercial rainbow trout population and found that whole-genome selection can substantially improve the genetic gains to increase resistance to this disease in rainbow trout aquaculture. In the current study, we conducted whole genome association analysis and identified 10 chromosome regions that harbor genes with moderate effect on IHNV resistance, indicating that the trait is controlled by many genes with small to moderate effect in the CSF population. We also found through simulation of real data that genomic selection can substantially improve the efficiency of selective breeding for IHNV resistance in this population over the traditional pedigree-based approach. Taken together, the results of this study suggest that whole genome-enabled selection methods will be more effective than conventional pedigree-based and marker-assisted selection methods for improving the genetic resistance of rainbow trout to IHNV in this important commercial rainbow trout breeding population.

Technical Abstract: Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods (CSF), Inc. has been applying traditional pedigree-based selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. The aims of this study were to (1) elucidate the genetic architecture of IHNV resistance in this commercial breeding population performing genome-wide association studies (GWAS) with two multiple regression single-step methods, and (2) assess if genomic selection can improve the accuracy of selecting genetically superior breeders over traditional pedigree-based selection method. A total of 10 moderate effect quantitative trait loci (QTL) associated with resistance to IHNV which jointly explained up to 42% of the genetic variance were detected in this study. Only three of the 10 QTL were detected by both the single-step Bayesian multiple regression (ssBMR) and the weighted single-step GBLUP (wssGBLUP) methods. The accuracy of animal genetic merit prediction with genome-enabled method wssGBLUP (0.33-0.39) was substantially better than with traditional pedigree-based method (0.13-0.24). Our genome-wide scan for QTL associated with IHNV resistance revealed that genetic resistance to IHNV is controlled by the oligogenic inheritance of up to 10 moderate effect QTL and many small effect genes in this commercial population. Taken together, the results of this study suggest that whole genome-enabled selection methods will be more effective than conventional pedigree-based and marker-assisted selection methods for improving the genetic resistance of rainbow trout to IHNV in this commercial rainbow trout breeding population.