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Title: Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle

item Kim, Eui-Soo
item Cole, John
item Huson, Heather
item Wiggans, George
item Van Tassell, Curtis - Curt
item CROOKER, BRIAN - University Of Minnesota
item Liu, Ge - George
item DA, YANG - University Of Minnesota
item Sonstegard, Tad

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2013
Publication Date: 11/14/2013
Publication URL:
Citation: Kim, E., Cole, J.B., Huson, H.J., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y., Sonstegard, T.S. 2013. Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle. PLoS One. DOI: 10.1371/journal.pone.0080813.

Interpretive Summary: Previous studies in livestock looking for human-directed selection for increased productivity in livestock were done using only recent or current generations of animals within a breed. In contrast, our study attemps to identify these signatures of selection by looking at regions or runs of homozygosity (ROH) of commercial Holstein cattle with that of a founding Hostein population that has been maintained the same levels of milk yield since the 1960's in Minnesota, USA. The unselected Holstein population is a unique resource population, providing information about the ROH status before intensive selection initiated in the 1960's, which could give an insight of the recent selection and differ from the previous studies of the Holstein selection signatures in the other regions. Also, the other recent studies used different methods to find signatures and analyzed only the commercial Holstein cattle selected for high productivity in Germany or Israel. The result of this work shows regions of the genome conferring increased milk production, which can be used to identify gene variations involed in production efficiency. This information is useful for understanding the biology of milk production, developing biotechnology strategies for genome editing of other cattle breeds, or increasing accuracy of selection through genome selection.

Technical Abstract: Genome signatures of artifical selection in U.S. Holstein cattle were identified by comparing changes in estimated haplotype homozygosity in a resource population born between 1953 and 2008. The intensive selection programs for milk made possible by mass artificial insemination have increased similarity of Holsteins tremendously since the 1960s. This migration of alleles has caused certain regions of the genome to have runs of homozygosity (ROH)occasionally spanning millioms of continuous base pairs at a specific locus. The ROH regions were used to find signatures of selection and to estimate the inbreeding coefficient for Holsteins. The comparisons of genomic autozygosity between selected and unselected groups indicated significant differences with respect to overall ROH and the distribution of ROH. Artificial selection has increased overall autozygosity across the genome, whereas the autozygosity in the unselected group has not changed significantly for most of the chromosomes. In addition, the ROH frequency in the selected group is more variable across the genome in comparison to a more even distribution of ROH in unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes including BTA2, 7, and 20 in the selected Holstein group. Many of the selection signatures were associated with QTL effects on dairy cattle traits, particularly milk, fat, and protein yeild of contemporary U.S. Holstein cattle over the past 40 years.