In animal breeding, parents of the next generation are usually selected in multiple stages, and the initial stages of this selection are called preselection. Preselection reduces the information available for subsequent evaluation of preselected animals and this sometimes leads to bias. The objective of this study was to establish the minimum information required to subsequently evaluate genomically preselected animals without bias arising from preselection, with single-step genomic best linear unbiased prediction (ssGBLUP). We simulated a nucleus of a breeding program in which a recent population of 15 generations was produced. In each generation, parents of the next generation were selected in a single-stage selection based on pedigree BLUP. However, in generation 15, 10% of male and 15% of female offspring were preselected on their genomic estimated breeding values (GEBV). These GEBV were estimated using ssGBLUP, including the pedigree of all animals in generations 0-15, genotypes of all animals in generations 13-15 and phenotypes of all animals in generations 11-14. In subsequent ssGBLUP evaluation of these preselected animals, genotypes and phenotypes from various groups of animals were excluded one after another. We found that GEBV of the preselected animals were only estimated without preselection bias when genotypes and phenotypes of all animals in generations 13 and 14 and of the preselected animals were included in the subsequent evaluation. We also found that genotypes of the animals discarded at preselection only helped in reducing preselection bias in GEBV of their preselected sibs when genotypes of their parents were absent or excluded from the subsequent evaluation. We concluded that to prevent preselection bias in subsequent ssGBLUP evaluation of genomically preselected animals, information representative of the reference data used in the evaluation at preselection and genotypes and phenotypes of the preselected animals are needed in the subsequent evaluation.

中文翻译：

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在随后对基因组预选动物的单步基因组 BLUP 评估中避免预选偏差

在动物育种中，通常分多个阶段选择下一代的亲本，这种选择的初始阶段称为预选。预选减少了可用于对预选动物进行后续评估的信息，这有时会导致偏差。本研究的目的是建立随后评估基因组预选动物所需的最少信息，而不会因预选而产生偏差，并采用单步基因组最佳线性无偏预测 (ssGBLUP)。我们模拟了繁殖计划的核心，其中产生了 15 代的最近种群。在每一代中，基于谱系 BLUP 在单阶段选择中选择下一代的父母。然而，在第 15 代，10% 的雄性和 15% 的雌性后代是根据其基因组估计育种值 (GEBV) 进行预选的。这些 GEBV 是使用 ssGBLUP 估计的，包括第 0-15 代所有动物的谱系、第 13-15 代所有动物的基因型和第 11-14 代所有动物的表型。在随后对这些预选动物的 ssGBLUP 评估中，来自不同动物组的基因型和表型被一个接一个地排除在外。我们发现，当第 13 代和第 14 代的所有动物以及预选动物的基因型和表型被纳入后续评估时，预选动物的 GEBV 仅在没有预选偏差的情况下进行估计。我们还发现，当父母的基因型不存在或被排除在随后的评估之外时，在预选时丢弃的动物的基因型仅有助于减少其预选同胞的 GEBV 的预选偏差。我们得出结论，为了防止在随后的基因组预选动物的 ssGBLUP 评估中出现预选偏差，在随后的评估中需要代表预选评估中使用的参考数据以及预选动物的基因型和表型的信息。