The Holstein Y-Chromosome: Only Two Y-Lineages Survived in North America

Holsteins are the most numerous dairy cattle breed in the world and have undergone intensive selection for improving milk production and conformation, which leads to the reduction of the effective population size (Ne) and a reduced genetic diversity. The objective of this study was to investigate Ne of the Holstein Y-chromosomes and the effects of the limited Y-chromosome lineages on male reproduction. Paternal pedigree of 62,897 Holstein bulls born during 1950-2013 in North America and 220,872 bulls registered in Interbull were analyzed. The results indicated that the number of Y-chromosome lineages in Holsteins has undergone a dramatic decrease during 1950-2013 as a consequence of artificial selection and the application of artificial insemination (AI) technology. All current Holstein AI bulls in North America are the descendants of only two ancestors born in 1880. These two ancestral Y-lineages are continued through three dominant pedigrees from the 1960s, namely Pawnee Farm Arlinda Chief, Round Oak Rag Apple Elevation, and Penstate Ivanhoe Star, with a contribution of 48.78%, 51.06% and 0.16% to the population in the 2010s, respectively. The genetic variations in the two ancestral Y-lineages were evaluated among 257 bulls by determining the copy number variations (CNVs) of three Y-linked gene families, PRAMEY, HSFY and ZNF280BY. No significant difference was found between the two ancestral Y-lineages although large CNVs were observed within each lineage. This study suggests minimal genetic diversity on the Y-chromosome in Holsteins, and provides a base for investigating the impact of the extremely limited number of Y-lineages on male reproduction.