Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows

Dzianis Prakapenka, Zuoxiang Liang, Yang Da

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A genome-wide association study (GWAS) of age at first calving (AFC) using 813,114 first lactation Holstein cows and 75,524 SNPs identified 2063 additive effects and 29 dominance effects with p-values < 10−8. Three chromosomes had highly significant additive effects in the regions of 7.86–8.12 Mb of Chr15, 27.07–27.48 Mb and 31.25–32.11 Mb of Chr19, and 26.92–32.60 Mb of Chr23. Two of the genes in those regions were reproductive hormone genes with known biological functions that should be relevant to AFC, the sex hormone binding globulin (SHBG) gene, and the progesterone receptor (PGR) gene. The most significant dominance effects were near or in EIF4B and AAAS of Chr05 and AFF1 and KLHL8 of Chr06. All dominance effects were positive overdominance effects where the heterozygous genotype had an advantage, and the homozygous recessive genotype of each SNP had a very negative dominance value. Results from this study provided new evidence and understanding about the genetic variants and genome regions affecting AFC in U.S. Holstein cows.

Original languageEnglish (US)
Article number7109
JournalInternational journal of molecular sciences
Issue number8
StatePublished - Apr 2023

Bibliographical note

Funding Information:
This research was supported by the National Institutes of Health’s National Human Genome Research Institute, grant R01HG012425 as part of the NSF/NIH Enabling Discovery through GEnomics (EDGE) Program; grant 2020-67015-31133 from the USDA National Institute of Food and Agriculture; and project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funding Information:
Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the dairy genomic evaluation data. The Ceres and Atlas high-performance computing systems of USDA-ARS were used for the data analysis. Paul VanRaden, Steven Schroeder, and Ransom Baldwin are acknowledged for help with the use of the CDCB data and USDA-ARS computing facilities. The use of the USDA-ARS computers in this research was supported by USDA-ARS projects 8042-31000-002-00-D and 8042-31000-001-00-D.

Publisher Copyright:
© 2023 by the authors.


  • GWAS
  • SNP
  • additive effect
  • age at first calving
  • dominance effect
  • reproductive hormone

PubMed: MeSH publication types

  • Journal Article


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