We tested the premise that optimum-contribution selection with pedigree relationships to control inbreeding (POCS) realises at least as much true genetic gain as optimum-contribution selection with genomic relationships (GOCS) at the same rate of true inbreeding. We used stochastic simulation to estimate rates of true genetic gain realised by POCS and GOCS at a 0.01 rate of true inbreeding in three breeding schemes with best linear unbiased predictions of breeding values based on pedigree (PBLUP) and genomic (GBLUP) information. The three breeding schemes differed in number of matings and litter size. Selection was for a single trait with a heritability of 0.2. The trait was controlled by 7702 biallelic quantitative-trait loci (QTL) that were distributed across a 30-M genome. The genome contained 54,218 biallelic markers that were used in GOCS and GBLUP. A total of 6012 identity-by-descent loci were placed across the genome in base populations. Unique alleles at these loci were used to calculate rates of true inbreeding. Breeding schemes were run for 10 discrete generations. Selection candidates were genotyped and phenotyped before selection. POCS realised more true genetic gain than GOCS at a 0.01 rate of true inbreeding in all combinations of breeding scheme and prediction method. POCS realised 14 to 33% more true genetic gain than GOCS with PBLUP in the three breeding schemes. It realised 1.5 to 5.7% more true genetic gain than GOCS with GBLUP. POCS realised more true genetic gain than GOCS because it managed expected genetic drift without restricting selection at QTL. By contrast, GOCS penalised changes in allele frequencies at markers that were generated by genetic drift and selection. Because these marker alleles were in linkage disequilibrium with QTL alleles, GOCS restricted changes in allele frequencies at QTL. This provides little incentive to use GOCS and highlights that we have more to learn before we can control inbreeding using genomic relationships in selective-breeding schemes. Until we can do so, POCS remains a worthy method of optimum-contribution selection because it realises more true genetic gain than GOCS at the same rate of true inbreeding.

中文翻译：

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在最佳贡献选择中控制亲缘关系的谱系关系比基因组关系实现更多的遗传增益

我们测试了这样一个前提，即具有相同血统关系的最佳贡献选择来控制近交（POCS），在相同的真实近亲繁殖率下，至少可以实现与具有基因组关系的最佳贡献选择（GOCS）一样多的真实遗传增益。我们使用随机模拟来估计POCS和GOCS在三种育种方案中以0.01的真实近交率实现的真实遗传增益的速率，并基于谱系（PBLUP）和基因组（GBLUP）信息对育种值进行最佳线性无偏预测。三种育种方案的交配数量和窝数不同。选择是针对遗传度为0.2的单个性状。该性状由分布在30-M基因组中的7702个双等位基因定量性状基因座（QTL）控制。基因组包含54 GOCS和GBLUP中使用了218个双等位基因标记。在整个基因组中，共有6012个通过血统鉴定的基因座位于基本种群中。在这些基因座上的独特等位基因被用来计算真实近交的比率。育种计划运行了10个离散世代。在选择之前，对候选基因进行基因分型和表型化。在育种方案和预测方法的所有组合中，POCS以0.01的真实近交率实现了比GOCS更高的真实遗传增益。在这三个育种方案中，POCS实现的真实遗传增益比使用PBLUP的GOCS高出14％至33％。与使用GBLUP的GOCS相比，它实现了真正的遗传增益1.5至5.7％。POCS实现了比GOCS更多的真实遗传增益，因为它可以控制预期的遗传漂移而不限制QTL的选择。相比之下，GOCS惩罚了由遗传漂移和选择产生的标记处等位基因频率的变化。由于这些标记等位基因与QTL等位基因处于连锁不平衡状态，因此GOCS限制了QTL等位基因频率的变化。这几乎没有动机来使用GOCS，并且强调了在选择育种方案中使用基因组关系控制近交之前，我们还有很多东西要学习。在我们做到这一点之前，POCS仍然是最佳贡献选择的一种有价值的方法，因为在相同的真实近交率下，POCS比GOCS可以实现更多的真实遗传增益。这几乎没有动机来使用GOCS，并且强调了在选择育种方案中使用基因组关系控制近交之前，我们还有很多东西要学习。在我们做到这一点之前，POCS仍然是一种有价值的最佳贡献选择方法，因为在相同的真实近交率下，POCS比GOCS可以实现更多的真实遗传增益。这几乎没有动机来使用GOCS，并且强调了在选择育种方案中使用基因组关系控制近交之前，我们还有很多东西要学习。在我们做到这一点之前，POCS仍然是最佳贡献选择的一种有价值的方法，因为在相同的真实近交率下，POCS比GOCS可以实现更多的真实遗传增益。