Assessing accuracy of genomic predictions for resistance to infectious hematopoietic necrosis virus with progeny testing of selection candidates in a commercial rainbow trout breeding population

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

Submitted to: Frontiers in Veterinary Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2020
Publication Date: 11/5/2020
Citation: Vallejo, R.L., Fragomeni, B.O., Cheng, H., Gao, G., Long, R., Shewbridge, K., Macmillan, J.R., Towner, R., Palti, Y. 2020. Assissing accuracy of genomic predictions for resistance to infectious hematopoietic necrosis virus with progeny testing of selection candidates in a commercial rainbow trout breeding population. Frontiers in Veterinary Science. 7:590048. https://doi.org/10.3389/fvets.2020.590048.
DOI: https://doi.org/10.3389/fvets.2020.590048

Interpretive Summary: Infectious hematopoietic necrosis is a viral disease of salmonid fish, and under intensive aquaculture conditions can cause significant mortality and economic losses because avoidance and control strategies for the disease are limited. Improving the resistance of a population to the virus using traditional family-based selective breeding has shown promise. Furthermore, using genome-enabled approaches for selective breeding for traits that cannot be measured directly in the potential breeders, like disease resistance, holds great potential as it uses an individual animal’s DNA sequence to predict genetic merit. In the current study, we compared the accuracy of genetic merit predictions among several genome-enabled approaches and the traditional family-based selective breeding approach using disease resistance data from a commercial rainbow trout breeding program. This study provides scientists with a better understanding of the genetic control of disease resistance in rainbow trout and demonstrates that genome-enabled selection can be more effective than traditional family-based selection in improving the resistance of a rainbow trout population to the infectious hematopoietic necrosis virus.

Technical Abstract: Infectious hematopoietic necrosis (IHN) is an economically important disease of salmonid fish caused by the IHN virus (IHNV). Under commercial aquaculture conditions, IHNV can cause significant mortality and losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been conducting family-based selective breeding to increase genetic resistance to IHNV in their rainbow trout breeding program. In a previous study we used siblings cross-validation to assess the accuracy of genomic prediction (GP) for IHNV resistance in this breeding population. In the current report, we used empirical progeny testing data to evaluate whether genomic selection (GS) can improve GP accuracy over traditional pedigree-based best linear unbiased prediction (PBLUP). We found that the GP accuracy with ssGBLUP outperformed PBLUP by 15% (from 0.33 to 0.38). Furthermore, we found that ssGBLUP had higher GP accuracy than wssGBLUP and ssBMR models which supports our previous findings that the underlying liability of genetic resistance against IHNV in this breeding population might be polygenic. Our results show that GS can be more effective than the traditional PBLUP model for improving genetic resistance against IHNV in this commercial rainbow trout breeding population. However, the margin of improvement from GS over PBLUP can be higher than 15% and through comparison with another study we discuss aspects of the experimental design that can be modified to further improve GP accuracy.