Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma, Tad S. Sonstegard, John B. Cole, Curtis P. Vantassell, George R. Wiggans, Brian A. Crooker, Cheng Tan, Dzianis Prakapenka, George E. Liu, Yang Da

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Background: The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical power for identifying high-confidence SNP effects. Utilizing these unique resources, we aimed to identify genome changes affected by selection since 1964. Results: Direct comparison of genome-wide SNP markers between a Holstein line unselected since 1964 and contemporary Holsteins showed that the 40 years of artificial selection since 1964 resulted in genome landscape changes. Among the regions affected by selection, the regions containing 198 genes with fertility functions had a larger negative correlation than that of all SNPs between the SNP effects on milk yield and daughter pregnancy rate. These results supported the hypothesis that hitchhiking of genetic selection for milk production by negative effects of fertility genes contributed to the unintended declines in fertility since 1964. The genome regions subjected to selection also contained 67 immunity genes, the bovine MHC region of Chr23 with significantly decreased heterozygosity in contemporary Holsteins, and large gene clusters including T-cell receptor and immunoglobulin genes. Conclusions: This study for the first time provided direct evidence that genetic selection for milk production affected fertility and immunity genes and that the hitchhiking of genetic selection for milk production by negative fertility effects contributed to the fertility declines since 1964, and identified a large number of candidate fertility and immunity genes affected by selection. The results provided novel understanding about genome changes due to artificial selection and their impact on fertility and immunity genes and could facilitate developing genetic methods to reverse the declines in fertility and immunity in Holstein cattle.

Original languageEnglish (US)
Article number128
JournalBMC Genomics
Issue number1
StatePublished - Feb 11 2019

Bibliographical note

Funding Information:
This research was supported by USDA National Institute of Food and Agriculture, Grant no. 2008–35205-18846, 2011–67015-30333, 2016–67015-24886 and 2018– 67015-28128, project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota, USDA-ARS project 8042–31000–002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals”, and USDA-ARS project 8042–31000–001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection”. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2019 The Author(s).


  • Fertility
  • Genetic selection
  • Genome landscape
  • Immunity
  • Milk production


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