Genetic Variation and the Distribution of Variant Types in the Horse

S. A. Durward-Akhurst, R. J. Schaefer, B. Grantham, W. K. Carey, J. R. Mickelson, M. E. McCue

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Genetic variation is a key contributor to health and disease. Understanding the link between an individual’s genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.

Original languageEnglish (US)
Article number758366
JournalFrontiers in Genetics
StatePublished - Dec 2 2021

Bibliographical note

Funding Information:
This work was supported by: USDA NIFA-AFRI Project 2017-67015-26296: Tools to Link Phenotype to Genotype in the Horse, The American Quarter Horse Association, and a University of Minnesota Multistate grant. Salary support for SD-A was provided by an American College of Veterinary Internal Medicine Foundation fellowship, by a T32 Institutional Training Grant in Comparative Medicine and Pathology (5T320D010993-12), by the 2019 Elaine and Bertram Klein Development Award, and a Morris Animal Foundation Postdoctoral Research Fellowship (D20EQ-403).

Publisher Copyright:
Copyright © 2021 Durward-Akhurst, Schaefer, Grantham, Carey, Mickelson and McCue.


  • breed differences
  • equine
  • genetic variation
  • genetics
  • variant discovery
  • whole genome sequence


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