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.

中文翻译：

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全基因组关联分析和基因组启用的育种值预测值的准确性，这些商业值可用于商业虹鳟鱼育种种群对传染性造血坏死病毒的抗性。

背景技术传染性造血坏死（IHN）是由IHN病毒（IHNV）引起的鲑鱼的疾病。在集约化水产养殖条件下，IHNV可能导致大量死亡和经济损失。目前，尚没有经过验证且具有成本效益的IHNV控制方法。Clear Springs Foods，Inc.在其虹鳟鱼育种计划中一直在应用选择性育种来提高对IHNV的遗传抗性。这项研究的目的是通过使用多重回归单步法进行全基因组关联研究（GWAS）来阐明该商业人群中IHNV耐药性的遗传结构，并评估基因组选择是否可以提高遗传优势预测的准确性。传统的基于谱系的最佳线性无偏预测（PBLUP），使用交叉验证分析。结果在我们的GWAS中检测到了十个与IHNV抗性相关的中效定量性状基因座（QTL），共同解释了多达42％的累加遗传变异。单步贝叶斯多元回归（ssBMR）和加权单步GBLUP（wssGBLUP）方法均检测到10个QTL中的三个。wssGBLUP（0.33-0.39）预测育种价值的准确性明显优于PBLUP（0.13-0.24）。结论我们对QTL进行的全基因组全面扫描显示，在该商业虹鳟繁殖种群中，对IHNV的遗传抗性受多达10个中等效果QTL和许多小影响基因座的寡聚遗传控制。在一起