In commercial fish, dominance effects could be exploited by predicting production abilities of the offspring that would be generated by different mating pairs and choosing those pairs that maximise the average offspring phenotype. Consequently, matings would be performed to reduce inbreeding depression. This can be achieved by applying mate selection (MS) that combines selection and mating decisions in a single step. An alternative strategy to MS would be to apply minimum coancestry mating (MCM) after selection based on estimated breeding values. The objective of this study was to evaluate, by computer simulations, the potential benefits that can be obtained by implementing MS or MCM based on genomic data for exploiting dominance effects when creating commercial fish populations that are derived from a breeding nucleus. The selected trait was determined by a variable number of loci with additive and dominance effects. The population consisted of 50 full-sib families with 30 offspring each. Males and females with the highest estimated genomic breeding values were selected in the nucleus and paired using the MCM strategy. Both MCM and MS were used to create the commercial population. For a moderate number of SNPs, equal or even higher mean phenotypic values are obtained by selecting on genomic breeding values and then applying MCM than by using MS when the trait exhibited substantial inbreeding depression. This could be because MCM leads to high levels of heterozygosity across the whole genome, even for loci affecting the trait that are in linkage equilibrium with the SNPs. In contrast, MS specifically promotes heterozygosity for SNPs for which a dominance effect has been detected. In most scenarios, for the management of aquaculture breeding programs it seems advisable to follow the MCM strategy when creating the commercial population, especially for traits with large inbreeding depression. Moreover, MCM has the appealing property of reducing inbreeding levels, with a corresponding reduction in inbreeding depression for traits beyond those included in the selection objective.

中文翻译：

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在水产养殖物种的基因组选择方案中发挥优势的最佳交配设计

在商品鱼中，可以通过预测将由不同交配对产生的后代的生产能力，并选择那些可使平均后代表型最大化的对来发挥优势作用。因此，将进行交配以减少近交衰退。这可以通过在单个步骤中应用将选择和配对决策结合起来的配合选择（MS）来实现。MS的替代策略是在选择后根据估计的育种值应用最小祖先交配（MCM）。这项研究的目的是通过计算机模拟评估通过基于基因组数据实施MS或MCM来获得潜在利益，这些利益可在创建源自繁殖核的商业鱼种群时利用基因组数据来发挥优势作用。选定的性状由具有加性和优势效应的可变位点决定。人口由50个同胞家庭组成，每个家庭有30个后代。在核中选择估计基因组育种值最高的雄性和雌性，并使用MCM策略进行配对。MCM和MS均用于创建商业人群。对于中等数量的SNP，当性状表现出明显的近交衰退时，通过选择基因组育种值，然后应用MCM，比使用MS可获得相等甚至更高的平均表型值。这可能是因为，即使对于影响与SNP连锁平衡的性状的基因座，MCM也会在整个基因组中导致高水平的杂合性。相反，MS特异地增强了已检测到优势作用的SNP的杂合性。在大多数情况下，对于水产养殖育种计划的管理，建议在创建商业种群时遵循MCM策略，尤其是对于近交抑郁大的性状。此外，MCM具有降低近交水平的吸引人的特性，与选择目标中所包括的特征相比，其近交沮丧程度相应降低。