Abstract
BackgroundInfectious 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.ResultsTen 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).ConclusionsOur 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.
Highlights
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV)
quantitative trait loci (QTL) associated with IHNV resistance Fifty-one 1-Mb windows that explained more than 1% explained additive genetic variance (EGV) were detected
These windows were used to define 21 QTL regions, of which were categorized as QTL associated with IHNV resistance (EGV ≥ 2%) (QTL2.2, 4.1, 4.2, 6.1, 16.1, 17.1, 21.1, 25.1, 26.1 and 28.1) and as QTL with suggestive association (1% ≤ EGV < 2%) (QTL 1.1, 2.1, 3.1, 5.1, 5.2, 8.1, 8.2, 14.1, 15.1, 25.2 and 29.1)
Summary
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). IHNV can cause significant mortality and economic losses. There is no proven and cost-effective method for IHNV control. Infectious hematopoietic necrosis (IHN) is an economically important disease of salmonid fish that is caused by IHN virus (IHNV), which is a single-stranded negative-sense RNA rhabdovirus [1]. Under intensive conditions of aquaculture, IHNV can cause significant mortality and losses at most stages of production [6, 7]. The development of rainbow trout strains with genetic resistance to IHNV can aid in improving animal welfare and in decreasing the economic losses that are caused by this highly infectious disease to aquaculture production
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