The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited studies on the specific genomic regions causing the observed negative association with the trait of interest. Our aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that display negative associations with production and fertility traits and to quantify the effects of these identified ROH genotypes. In total, 50,575 genotypes based on a 50K single nucleotide polymorphism (SNP) array and 259,871 pedigree records were available. Of these 50,575 genotypes, 46,430 cows with phenotypic records for production and fertility traits and having a first calving date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were fitted into an animal mixed model as fixed effects to determine their effect on production and fertility traits. In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production and fertility traits, respectively, at a 1% genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, 14 and 19 for both production and fertility traits. For production traits, the average of all the unfavorably identified unique ROH genotypes effects were estimated to decrease milk yield by 247.30 kg, fat yield by 11.46 kg and protein yield by 8.11 kg. Similarly, for fertility traits, an average 4.81-day extension in first service to conception, a 0.16 increase in number of services, and a − 0.07 incidence in 56-day non-return rate were observed. Furthermore, a ROH region located on bovine chromosome 19 was identified that, when homozygous, had a negative effect on production traits. Signatures of selection proximate to this region have implicated GH1 as a potential candidate gene, which encodes the growth hormone that binds the growth hormone receptor. This observed negative effect could be a consequence of unfavorable alleles in linkage disequilibrium with favorable alleles. ROH genotypes with unfavorable effects on production and fertility traits were identified within and across multiple traits on most chromosomes. These identified ROH genotypes could be included in mate selection programs to minimize their frequency in future generations.

中文翻译：

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鉴定对加拿大荷斯坦牛的生产和生育性状有不利影响的独特 ROH 区域

基因组信息的出现和基因分型成本的降低导致使用基因组信息来估计基因组近亲繁殖，作为谱系近亲繁殖的替代方法。使用基因组测量，已经观察到基因组近亲繁殖对生产和生育性状的影响。然而，对导致观察到的与感兴趣的性状负相关的特定基因组区域的研究有限。我们的目标是确定给定基因组窗口中存在的独特纯合子 (ROH) 基因型，这些基因型与生产和生育性状呈负相关，并量化这些已确定的 ROH 基因型的影响。总共有 50,575 个基于 50K 单核苷酸多态性 (SNP) 阵列的基因型和 259,871 条谱系记录可用。在这 50,575 个基因型中，46 个，有 430 头奶牛具有生产和繁殖性状的表型记录，并且第一次产犊日期在 2008 年至 2018 年之间。使用滑动窗口方法鉴定的独特 ROH 基因型作为固定效应拟合到动物混合模型中，以确定它们对生产和生育性状的影响。总共以 1% 的基因组错误发现率分别鉴定了 133 和 34 个具有不利影响的独特 ROH 基因型的生产和生育性状。大多数这些 ROH 区域位于牛染色体 8、13、14 和 19 上，用于生产和生育性状。对于生产性状，估计所有不利识别的独特 ROH 基因型影响的平均值使产奶量减少 247.30 公斤，脂肪产量减少 11.46 公斤，蛋白质产量减少 8.11 公斤。同样，对于生育性状，观察到首次服务至受孕平均延长 4.81 天，服务数量增加 0.16，56 天不复发率增加 - 0.07。此外，确定了位于牛 19 号染色体上的 ROH 区域，当纯合时，对生产性状有负面影响。该区域附近的选择特征表明 GH1 是一个潜在的候选基因，它编码与生长激素受体结合的生长激素。这种观察到的负面影响可能是不利等位基因与有利等位基因连锁不平衡的结果。在大多数染色体上的多个性状内和跨多个性状鉴定出对生产和生育性状具有不利影响的 ROH 基因型。