Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland

Significant associations were detected for milk yield, fat yield, protein yield, fat percentage, protein percentage and somatic cell score using separate single-locus, frequentist and multi-locus, Bayesian approaches. These associations were detected using two separate populations of Holstein-Friesian sires and cows. In total, 1,529 and 37 associations were detected in the sires using a single SNP regression and a Bayesian method, respectively. There were 103 associations in common between the sires and cows across all the traits. As well as detecting associations within known QTL regions, a number of novel associations were detected; the most notable of these was a region of chromosome 13 associated with milk yield in the population of Holstein-Friesian sires.A total of 276 of novel SNPs were detected in the sires using a single SNP regression approach. Although obvious candidate genes may not be initially forthcoming, this study provides a preliminary framework upon which to identify the causal mechanisms underlying the various milk production traits and somatic cell score. Consequently this will deepen our understanding of how these traits are expressed.Dairy production is an economically important sector of global agriculture with the top 10 leading dairy companies turning over in excess of $114 billion in 2009 [1]. Dairy cows account for 84% of global dairy output [1] so consequently there is great interest placed upon the production potential and health of these animals. Until recently, the majority of international dairy breeding programmes selected solely for increased milk production, however, breeding goals have diversified to include health and functional traits in an effort to minimise and reverse the decline in these traits [2]. Prominent among these health-related traits is mastitis (commonly measured using somatic cell score (SCS) as an indicator trait), which is one of the most important and costly production diseases in the dairy industry. Selection