Genetics Selection Evolution (Aug 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

  • Roger L. Vallejo,
  • Hao Cheng,
  • Breno O. Fragomeni,
  • Kristy L. Shewbridge,
  • Guangtu Gao,
  • John R. MacMillan,
  • Richard Towner,
  • Yniv Palti

DOI
https://doi.org/10.1186/s12711-019-0489-z
Journal volume & issue
Vol. 51, no. 1
pp. 1 – 14

Abstract

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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.