Genome Wide Association Analysis on Imputed High Density SNP Genotypes in the Italian and Swiss Brown Swiss Dairy Cattle Population for Milk Somatic Cell Count

Mastitis is one of the most costly diseases in dairy cattle and a huge concern to animal welfare. Milk Somatic Cell Count (MSCC) is an indirect measure widely used for years to select individuals to reduce mastitis susceptibility in dairy cattle. The purpose of this study was to identify regions underlying phenotypic variation for mastitis resistance in the Brown Swiss dairy cattle population. We report on a whole genome association study on a total of 2,979 mainly Italian-, Swiss- and US-Brown Swiss bulls imputed from Illumina’s Bovine 50k v1 and v2 SNP chip with FImpute to Illumina’s 777k chip for 628,415 SNPs with MAF > 0.5% anchored on the UMD3.1 autosome. Association testing with MSCC-EBVs for 2,834 bulls with EBV reliability greater than 0.3 provided by Interbull, was performed for 604,568 SNPs with MAF > 2% employing EMMAX as implemented in SVS7.7.8. Stratification was controlled by fitting a genomic relationship matrix, calculated as suggested by VanRaden based on all genome wide SNPs in the model. Success of stratification correction was empirically assessed via quantile-quantile plots. Significance was declared employing a false discovery rate approach. Several QTL regions were found across the genome. The most interesting regions were located on BTA6, BTA10, BTA13 and BTA19.

We thank Braunvieh Schweiz and ANARB for providing genotypes and Genotype pool Germany-Austria, Beltsville Agricultural Research Centre and LowInputBreeds, FP7 – project KBBE 222 632 for providing genotypes used for imputation. This study was supported by the FP7 project QUANTOMICS contract n. 222664-2.