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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #311606

Title: Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions

Author
item KIM, EUI-SOO - Iowa State University
item Sonstegard, Tad
item ROTHSCHILD, MAX - Iowa State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2015
Publication Date: 4/16/2015
Citation: Kim, E., Sonstegard, T.S., Rothschild, M. 2015. Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions. Biomed Central (BMC) Genomics. 16(1):302.

Interpretive Summary: Artificial selection based on quantitative genetics theory for animal breeding has dramatically increased dairy production in livestock. This selection was enabled by the extensive use of artificial insemination from a few superior Jersey bulls. In this study, we examined if levels of genomic homozygosity in specific genomic regions of modern Jersey cattle were associated with milk, fat, and protein yield traits under selection. The genomic homozygosity was determined using SNP data from the Illumina Bovine50K SNP chip. Our analysis revealed 25 genomic regions that have undergone a substantial change in autozygosity, and many of these regions are associated with milk production traits. Methods to determine the recency of these changes reveal that the more recent regions moving toward homozygosity are related to genes encoding proteins affecting milk protein yield. This result agrees with the use of a selection index since the 1970s that puts more weight on this protein yield due to the economic benefits to improved cheese production.

Technical Abstract: Genome signatures of artificial selection in U.S. Jersey cattle were identified by examining changes in haplotype homozygosity for a resource population of animals born between 1962 and 2005. Genetic merit of this population changed dramatically during this period for a number of traits, especially milk yield. The intense selection underlying these changes was achieved through extensive use of artificial insemination (AI), which also increased consanguinity of the population to a few superior Jersey bulls. As a result, allele frequencies are shifted for many contemporary animals, and in numerous cases to a homozygous state for specific genomic regions. The goal of this study was to identify those selection signatures that occurred after extensive use of AI (1960s). The shared haplotype segments or Runs of Homozygosity (ROH) often span millions of contiguous base pairs. When combined with animal birth year information, signatures of selection associated with economically important traits were identified and compared to results from an extended haplotype homozygosity analysis. Overall, our results reveal that more recent selection increased autozygosity across the entire genome, but some specific regions increased more than others. A genome-wide scan identified more than 25 regions with a substantial change in autozygosity. Haplotypes found to be associated with increased milk, fat and protein yield in U.S. Jersey cattle also consistently increased in frequency. The analyses used in this study was able to detect directional selection over the last few decades when livestock production records were available.