Subclinical mastitis (SM) is one of the most common diseases of cows in milk production herds caused by contagious and/or environmental pathogens. Since there are no visible abnormalities in the milk or udder, the detection of SM requires special diagnostic tests. Somatic cell count (SCC) is the most common test used to detect changes in milk due to the inflammatory process. Previously, we developed somatic cell count index (SCCI), a new method for the accurate prediction of milk yield losses caused by elevated SCC. The aim of this study was to identify new candidate genetic markers for SCCI in the Slovenian population of Brown Swiss (BS) cattle. For that purpose, we analyzed samples of BS cows, which were genotyped using single-nucleotide polymorphism (SNP) microarray ICBF International Dairy and Beef v3 (ICBF, Ireland) for a total of 53,262 SNP markers. After quality control, the set of 18,136 SNPs was used in association analysis. Our association analysis revealed that 130 SNPs were associated with SCCI, which were used for haplotype and overlap analysis. Haplotypes generated from the genotyped data for those 130 SNPs revealed 10 haplotype blocks among 22 SNPs. Additionally, all 130 SNPs, mastitis-related quantitative trait loci, and protein-coding genes are shown on the bovine genome. Overlap analysis shows that the majority of significantly associated SNPs (70) are intergenic, while 60 SNPs are mapped within, upstream, or downstream of the protein-coding genes. However, those genes can serve as strong candidate genes for the marker-assisted selection programs in our and possibly other populations of cattle.

中文翻译：

---

与棕色瑞士牛体细胞计数指数相关的基因

亚临床乳腺炎 ( SM ) 是产奶牛群中奶牛最常见的疾病之一，由传染性和/或环境病原体引起。由于牛奶或乳房没有明显的异常，检测 SM 需要特殊的诊断测试。体细胞计数 ( SCC ) 是最常用的测试，用于检测由于炎症过程引起的牛奶变化。此前，我们开发了体细胞计数指数 ( SCCI )，这是一种准确预测 SCC 升高引起的产奶量损失的新方法。本研究的目的是在斯洛文尼亚的瑞士布朗族 ( BS) 中鉴定新的 SCCI 候选遗传标记。) 牛。为此，我们分析了 BS 奶牛的样本，这些样本使用单核苷酸多态性 ( SNP) 芯片 ICBF International Dairy and Beef v3 (ICBF, Ireland) 共 53,262 个 SNP 标记。质量控制后，这组 18,136 个 SNP 用于关联分析。我们的关联分析显示 130 个 SNP 与 SCCI 相关，用于单倍型和重叠分析。从这 130 个 SNP 的基因分型数据生成的单倍型揭示了 22 个 SNP 中的 10 个单倍型块。此外，所有 130 个 SNP、乳腺炎相关数量性状基因座和蛋白质编码基因都显示在牛基因组上。重叠分析表明，大多数显着相关的 SNP (70) 是基因间的，而 60 个 SNP 位于蛋白质编码基因的内部、上游或下游。然而，