BACKGROUND Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein-Friesian cows. METHODS In total, 38,792 first-parity cows were included. Pedigree inbreeding ([Formula: see text]) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome ([Formula: see text]). RESULTS Inbreeding depression was observed, e.g. a 1% increase in [Formula: see text] was associated with a 36.3 kg (SE = 2.4) decrease in 305-day milk yield, a 0.48 day (SE = 0.15) increase in calving interval and a 0.86 unit (SE = 0.28) increase in somatic cell score for day 150 through to 400. These effects equalled - 0.45, 0.12 and 0.05% of the trait means, respectively. When [Formula: see text] was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When [Formula: see text] was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE = 0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE = 0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding). CONCLUSIONS Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.

中文翻译：

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由于荷兰荷斯坦-弗里斯兰奶牛的近亲和近亲繁殖而造成的近亲衰退。

背景技术近交会降低动物的生产能力（近交抑郁），但并不是所有的近交都被认为具有同等的危害性。由于选择会随着时间的推移减少有害等位基因的频率，因此最近的近交有望比古代的近交更具危害性。通过近交来提高选择效率，这一过程称为清除。我们的目标是调查近交和远古近交对荷兰荷斯坦-弗里斯兰奶牛的产量，繁殖力和乳房健康性状的影响。方法总共包括38792头第一胎母牛。计算了谱系近交（[公式：参见文本]），并基于基因组中的纯合性（ROH）区域，使用了75 k基因型数据来计算基因组近交（[公式：参见文本]）。结果观察到近亲衰退，例如[配方：305天的产奶量减少36.3千克（SE = 2.4），产犊间隔增加0.48天（SE = 0.15），体细胞天数增加0.86单位（SE = 0.28）从150到400。这些效果分别等于特征平均值的0.45％，0.12％和0.05％。当[公式：参见文字]分成基于世代的成分时，近代的近亲繁殖比单产远的几代具有更大的危害。当[公式：参见正文]分为新的和祖先的成分时，根据等位基因是否首次在后代中相同，新近交比祖先近交更加有害，特别是对于产量性状。例如，与0相比，新近交增加1％与305天的脂肪产量减少2.42 kg（SE = 0.41）相关。祖先近亲繁殖需增加03千克（SE = 0.71）。长ROH（近交）和短ROH（古代近交）的影响之间没有明显差异。结论观察到近交性抑郁症的产量，生育力和乳房健康性状。就产量性状和系谱而言，近代近交比远代近交有害，并且有清除的证据。在所有特征中，长期和短期的ROH都会导致近交衰退。在将来的工作中，应使用更高的密度信息和基因组时间序列在基因组水平上更详细地评估近亲繁殖和清除。结论观察到近交性抑郁症的产量，生育力和乳房健康性状。对于产量性状和基于系谱而言，近代近交比远代近交有害，并且有清除的证据。在所有特征中，长期和短期的ROH都会导致近交衰退。在将来的工作中，应使用更高的密度信息和基因组时间序列在基因组水平上更详细地评估近亲繁殖和清除。结论观察到近交性抑郁症的产量，生育力和乳房健康性状。就产量性状和系谱而言，近代近交比远代近交有害，并且有清除的证据。在所有特征中，长期和短期的ROH都会导致近交衰退。在将来的工作中，应使用更高的密度信息和基因组时间序列在基因组水平上更详细地评估近亲繁殖和清除。