Bull fertility is a key factor for successful reproductive performance in dairy cattle. Since the semen from a single bull can be used to inseminate hundreds of cows, one subfertile bull could have a major impact on herd reproductive efficiency. We have previously identified five genomic regions, located on BTA8 (72.2 Mb), BTA9 (43.7 Mb), BTA13 (60.2 Mb), BTA17 (63.3 Mb), and BTA27 (34.7 Mb), that show large dominance effects on bull fertility. Each of these regions explained about 5–8% of the observed differences in sire conception rate between Holstein bulls. Here, we aimed to identify candidate causal variants responsible for this variation using targeted sequencing (10 Mb per region). For each genomic region, two DNA pools were constructed from high-fertility and low-fertility Holstein bulls. The DNA-sequencing analysis included reads quality control (using FastQC), genome alignment (using BWA and ARS-UCD1.2), variant calling (using GATK) and variant annotation (using Ensembl). The sequencing depth per pool varied from 39× to 51×. We identified a set of nonsense mutations, missense mutations, and frameshift variants carried by low-fertility bulls. Notably, some of these variants were classified as strong candidate causal variants, i.e., mutations with deleterious effects located on genes exclusively/highly expressed in testis. Genes affected by these candidate causal variants include AK9, TTLL9, TCHP, and FOXN4. These results could aid in the development of novel genomic tools that allow early detection and culling of subfertile bull calves.

中文翻译：

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靶向测序揭示了奶牛不育的候选因果变异

公牛繁殖力是奶牛成功繁殖性能的关键因素。由于一头公牛的精液可用于对数百头母牛进行授精，因此一头低生育力公牛可能对牛群繁殖效率产生重大影响。我们之前已经确定了位于 BTA8 (72.2 Mb)、BTA9 (43.7 Mb)、BTA13 (60.2 Mb)、BTA17 (63.3 Mb) 和 BTA27 (34.7 Mb) 上的五个基因组区域，它们显示出对公牛生育力的巨大优势效应。这些区域中的每一个都解释了荷斯坦公牛之间大约 5-8% 的观察到的公牛受孕率差异。在这里，我们旨在使用靶向测序（每个区域 10 Mb）来确定导致这种变异的候选因果变异。对于每个基因组区域，从高生育率和低生育力的荷斯坦公牛。DNA 测序分析包括读取质量控制（使用 FastQC）、基因组比对（使用 BWA 和 ARS-UCD1.2）、变异调用（使用 GATK）和变异注释（使用 Ensembl）。每个池的测序深度从 39x 到 51x 不等。我们鉴定了一组由低生育力公牛携带的无义突变、错义突变和移码变异。值得注意的是，这些变异中的一些被归类为强候选因果变异，即具有有害影响的突变位于睾丸中排他性/高度表达的基因上。受这些候选因果变异影响的基因包括AK9、TTLL9、TCHP和FOXN4. 这些结果可能有助于开发新的基因组工具，这些工具可以及早发现和剔除不育的公牛犊。