Basal CD18 antigen levels in cow milk associates with copy number variation of Fc gamma receptors

High somatic cell count (SCC) in cows' milk is an indicator of poor milk quality and of mastitis that imposes significant economic losses to the dairy industry.We identified an informative haplotype of 15 SNPs in the centromeric end of BTA3 that was highly associated with CD18 SCCs (p<2.3×10-09). Within this region, examination of the network of genes interacting with ITGB2 (CD18) pointed to an Fc-gamma-receptor gene cluster, including FCGR2A (CD32). Sanger-sequence analysis of FCGR2A linked exon3 variation to CD18 counts. Indeed, meta-analysis of RNA-seq data revealed significant negative correlation (R=-0.51) between expression of CD32 and CD18 in milk. Assembly of DNA-seq reads uncovered FCGR copy-number variation and a variant designated V7. V7 was abundant in dairy cattle, probably reflecting adaptation to a selective pressure towards low SCCs in Holstein's milk.