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.

Roger L Vallejo,Breno O Fragomeni,Yniv Palti,Roseanna L Long,John R Macmillan,Kristy L Shewbridge,Guangtu Gao,Hao Cheng,Richard Towner

doi:10.3389/fvets.2020.590048

Abstract

Infectious hematopoietic necrosis (IHN) is an economically important disease of salmonid fish caused by the IHN virus (IHNV). Under industrial aquaculture settings, IHNV can cause substantial mortality and losses. Actually, there is no confirmed and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been performing family-based selective breeding to increase genetic resistance to IHNV in their rainbow trout breeding program. In an earlier study, we used siblings cross-validation to estimate the accuracy of genomic prediction (GP) for IHNV resistance in this breeding population. In the present report, we used empirical progeny testing data to evaluate whether genomic selection (GS) can improve the accuracy of breeding value predictions over traditional pedigree-based best linear unbiased predictions (PBLUP). We found that the GP accuracy with single-step GBLUP (ssGBLUP) outperformed PBLUP by 15% (from 0.33 to 0.38). Furthermore, we found that ssGBLUP had higher GP accuracy than weighted ssGBLUP (wssGBLUP) and single-step Bayesian multiple regression (ssBMR) models with BayesB and BayesC priors 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 either the traditional pedigree-based PBLUP model or the marker-assisted selection approach for improving genetic resistance against IHNV in this commercial rainbow trout population.

Highlights

Infectious hematopoietic necrosis (IHN) is an important disease of salmonid fish that is caused by IHN virus (IHNV), which is a single-stranded negative-sense RNA rhabdovirus [1]
The accuracy of breeding value (BV) predictions was higher for the genomic prediction (GP) models single-step genomic best linear unbiased prediction (GBLUP) (ssGBLUP) (0.38), wssGBLUP (0.35) and single-step Bayesian multiple regression (ssBMR)-BayesBπ (0.34) than for the pedigree-based pedigree-based BLUP (PBLUP) model (0.33), and the PBLUP and ssBMR-BayesCπ models had similar accuracy (Table 3)
We found that ssGBLUP had higher accuracy GP than wssGBLUP and ssBMR which suggest that the underlying liability to IHNV resistance might be polygenic

Summary

Introduction

Infectious hematopoietic necrosis (IHN) is an important disease of salmonid fish that is caused by IHN virus (IHNV), which is a single-stranded negative-sense RNA rhabdovirus [1]. The development of rainbow trout strains with genetic resistance to IHNV is needed for improving animal well-being and decreasing economic losses that are inflicted by this infectious viral induced disease to food aquaculture production [8]. We found moderate estimates of heritability for IHNV binary survival status (h2 = 0.25–0.28) and survival days to death (h2 = 0.23–0.33) in a commercial rainbow trout breeding population [8]. These reports suggest that rainbow trout strains with genetic resistance against IHNV can be developed by means of traditional family-based selective breeding. Selective breeding of a rainbow trout strain for resistance to IHNV has been conducted at the Clear Springs Foods Inc. (CSF) breeding program since the year 2000 [10], and the selection differential for resistance to IHNV has been on average 10% for the last eight generations between 2000 and 2016 [8]

Objectives

Methods

Results

Discussion

Conclusion