Genes associated with somatic cell count index in Brown Swiss cattle.

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.