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

Abstract

Background 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, Inc. has been applying selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. The goals of this study were to elucidate the genetic architecture of IHNV resistance in this commercial population by performing genome-wide association studies (GWAS) with multiple regression single-step methods and to assess if genomic selection can improve the accuracy of genetic merit predictions over conventional pedigree-based best linear unbiased prediction (PBLUP) using cross-validation analysis. Results Ten moderate-effect quantitative trait loci (QTL) associated with resistance to IHNV that jointly explained up to 42% of the additive genetic variance were detected in our GWAS. Only three of the 10 QTL were detected by both single-step Bayesian multiple regression (ssBMR) and weighted single-step GBLUP (wssGBLUP) methods. The accuracy of breeding value predictions with wssGBLUP (0.33–0.39) was substantially better than with PBLUP (0.13–0.24). Conclusions Our comprehensive genome-wide scan for QTL revealed that genetic resistance to IHNV is controlled by the oligogenic inheritance of up to 10 moderate-effect QTL and many small-effect loci in this commercial rainbow trout breeding population. Taken together, our results suggest that whole genome-enabled selection models will be more effective than the conventional pedigree-based method for breeding value estimation or the marker-assisted selection approach for improving the genetic resistance of rainbow trout to IHNV in this population.

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

“…Nonetheless, these results are in line with the range of previous heritability estimates for resistance to ISAV in Atlantic salmon (0.13-0.40; [23][24][25][26][27]). The genetic architecture of resistance to ISAV in this population was polygenic, and major QTL were not observed, as is common for disease resistance traits [56][57][58][59][60][61]. Yet, four genomic regions explaining > 2.5% of the genetic variation in resistance to ISAV were detected.…”

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

“…The additive genetic basis for IHNV resistance is evident from the moderate estimates of heritability for IHNV binary survival status (h 2 = 0.23-0.55) and survival days to death (h 2 = 0.02-0.20) in a steelhead trout population (2). Recently, we also found moderate estimates of heritability for IHNV binary survival status (h 2 = 0.25-0.28) and survival days to death (h 2 = 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.…”

“…IHNV is infectious to Pacific salmon and trout (Oncorhynchus spp. ), as well as to Atlantic salmon (Salmo salar) (2), and can cause significant mortality and losses at nearly all stages of production in commercial aquaculture settings (6)(7)(8). Currently, unfortunately, there is no confirmed and cost-effective method for IHNV prevention or treatment.…”

“…Currently, unfortunately, there is no confirmed and cost-effective method for IHNV prevention or treatment. Therefore, 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).…”

“…The process of selecting and developing IHNV-resistant strains is further complicated due to the high genetic variability of the IHN virus as revealed by phylogenetic and nucleotide sequence analyses of 84 IHNV isolates (9). Nevertheless, 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).…”