Haplotype-Based Selection Signature Analysis Using University Of Minnesota And Us Contemporary Holstein Cattle

Abstract

Artificial selection in dairy cattle since 1964 has achieved steady increase in milk production that was accompanied by unintended declines in fertility. We conducted selection signature analysis to identify genome changes due to the forty years of selection using direct comparison of 45,878 SNPs between Holstein cattle unselected since 1964 and contemporary Holsteins. The Holstein genome had a landscape change from the unselected to the elite contemporary Holsteins. About 31% of the genome was affected by the forty years of selection, and 230 regions had highly significant changes in long-range allele frequencies and genotypic heterozygosity. From these 230 regions, 197 genes with documented fertility functions mostly in mice and humans were identified, leading to the hypothesis that the unintended declines in fertility since 1964 was due to hitchhiking of selection by negative effects of fertility genes. The female-male ratio of the 197 fertility genes is approximately 5:4, indicating that the fertility problems in the contemporary Holstein population likely was due to decreased fertility in both females and males. The elite Holsteins were more heterozygous than their contemporaries in all thirty regions where the elite cows and their contemporaries had significant heterozygosity differences, including seven regions in or near large clusters of olfactory receptors, zinc fingers, cationic amino acid transporters, sialic acid-binding Ig-like genes, vomeronasal receptors, keratin genes, EMR2 receptors, and transfer RNA’s.