Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Anim Genet. 2021 Aug;52(4):509-513. doi: 10.1111/age.13089. Epub 2021 May 24.
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.
公牛的繁殖力是奶牛成功繁殖性能的关键因素。由于一头繁殖力低下的公牛可能会对整个牛群的繁殖效率产生重大影响，因此，单头公牛的精液可以用于数百头母牛的人工授精。我们之前已经确定了五个基因组区域，它们位于 BTA8（72.2Mb）、BTA9（43.7Mb）、BTA13（60.2Mb）、BTA17（63.3Mb）和 BTA27（34.7Mb）上，这些区域对公牛的繁殖力有很大的显性效应。每个区域解释了大约 5-8%的荷斯坦公牛的受胎率差异。在这里，我们旨在使用靶向测序（每个区域 10Mb）来识别导致这种变异的候选因果变异。对于每个基因组区域，从高繁殖力和低繁殖力的荷斯坦公牛中构建了两个 DNA 池。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 39×到 51×不等。我们鉴定了一组由低繁殖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，其中一些变异被归类为强候选因果变异，即位于睾丸中特异/高表达的基因上的具有有害效应的突变。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，从而能够早期检测和淘汰繁殖力低下的公牛。
