Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population. Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method. Validation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations. Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations.

中文翻译：

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两种虹鳟繁殖种群对性状基因座的定量性状基因座的全基因组定位和基因组预测的准确性

柱状病（CD）是美国虹鳟鱼水产养殖业中一个正在出现的问题。这项研究的目的是：（1）确定共同的基因组区域，以解释两个虹鳟（Oncorhynchus mykiss）种群对CD抗性的大部分累加遗传方差；（2）当使用基因组信息评估每个人群中感染柱状病毒的遗传潜力时，估计预测准确性的提高。调查了两个水产养殖种群：国家冷水和冷水水产养殖中心（NCCCWA）奇数年线和Troutlodge，Inc.的5月奇数年（TLUM）核繁殖种群。存活到浸没攻击后21天的鱼被记录为有抗性。单核苷酸多态性（SNP）基因型分别适用于来自NCCCWA和TLUM的1185和1137鱼类。使用加权单步基因组最佳线性无偏预测（BLUP）估计全基因组关联的SNP效应和方差。解释了超过1％的累加遗传变异的基因组区域被认为与对CD的抗性有关。通过五重交叉验证方案并使用线性回归方法计算预测能力。由于性状的二元性质，对调整表型的验证提供了接近零的预测准确性。与基于系谱的BLUP相比，使用从完整数据计算出的育种值作为基准，可将基因组模型的预测准确性提高约40％。位于NCCCWA种群中的六个染色体上的14个窗口与对CD的抗性相关，其中Omy 17染色体上的两个窗口共同解释了10％以上的累加遗传变异。在TLUM群体中，位于13个染色体上的26个窗口与对CD的抗性相关。两个种群之间只有四个相关的基因组区域与数量性状基因座（QTL）重叠。我们的研究结果表明，虹鳟对CD的抗性全基因组选择的潜力要比针对几个目标基因组区域的选择具有更大的潜力，这些目标基因组区域由于该性状的多基因结构而被发现与CD的抗性相关，并且因为QTL相关对CD有抗性的人不能为跨人群的选择决策提供足够的信息。