Genomic associations with somatic cell score in first-lactation Holstein cows

This genome-wide association study aimed to identify loci associated with lactation-average somatic cell score (LASCS) and the standard deviation of test-day somatic cell score (SCS-SD). It is one of the first studies to combine detailed phenotypic and genotypic cow data from research dairy herds located in different countries. The combined data set contained up to 52 individual test-days per lactation and thereby aimed to capture temporary increases in somatic cell score associated with infection. Phenotypic data for analysis consisted of 46,882 test-day records on 1,484 cows, and genotypic data consisted of 37,590 single nucleotide polymorphisms (SNP). Using an animal model, the associations between each individual SNP and the phenotypic data were estimated. To account for the risk of false positives, a false discovery rate threshold of 0.20 was set. The analyses showed that LASCS was significantly associated with a SNP on Bos taurus autosome (BTA) 4 and a SNP on BTA18. Likewise, SCS-SD was associated with this SNP on BTA18. In addition, SCS-SD significantly associated with a SNP on BTA6. Relatively few associations were found, suggesting that LASCS and SCS-SD are controlled by multiple loci distributed across the genome, each with a relatively small effect. Increased knowledge on genetic regulation of LASCS and SCS-SD may aid in identification of genes that play a role in mastitis resistance. Such knowledge helps us understand the genetic mechanisms leading to mastitis and in discovery of targets for mastitis therapeutics.