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Frontiers in genetics2018; 9; 249; doi: 10.3389/fgene.2018.00249

Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.

Abstract: Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di ) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.
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Publication Date: 2018-07-19 PubMed ID: 30105047PubMed Central: PMC6060370DOI: 10.3389/fgene.2018.00249Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article “Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations”, is an investigation of genetic and genomic factors influencing the performance of different groups within the American Quarter Horse breed. It employs genomic data to identify areas under positive evolutionary selection, understand the structure of haplotypes in each group, and recognize pertinent genes and biological pathways.

Objectives and Methodology

  • This research aims to uncover the underlying genetics contributing to the athletic performance of American Quarter Horses, focusing on distinct subgroups, including cutting, halter, racing, reining, western pleasure, and working cow.
  • Utilizing high-density genotype data available on 143 elite horses from these aforementioned subgroups, the study aims to identify genomic regions undergoing positive selection, explore the structure of haplotypes within these groups and identify candidate genes and biological pathways within regions of interest (ROIs).
  • The researchers carried out these analyses using two methods: a -based (- ) and haplotype-based (hapFLK). They also identified local haplotype structures and sharing within these groups using a method referred to as hapQTL.
  • The 65,000 Single Nucleotide Polymorphism (SNP) genotyping data was then imputed to 2 million SNPs to provide a finer level of genetic detail.

Results and Implications

  • The researchers identified regions of positive selection across all 31 autosomes (non-sex chromosomes) in horses. Of note, ROI on two chromosomes were identified by integrating results from all three analysis methods.
  • Upon further inspection of these ROIs, they identified multiple candidate genes potentially contributing to the performance in each subgroup. These genes were associated with key areas like skeletal muscle development, metabolism, and central nervous system development.
  • The biological pathways implicated by the candidate genes were then examined, providing insight into the functional aspects of these performance-related traits.
  • This research not only enhances the scientific understanding of genetic factors influencing performance traits in horses but also provides practical guidance for breeders. This knowledge can inform selective breeding practices for improved performance within the American Quarter Horse populations.

Cite This Article

APA
Avila F, Mickelson JR, Schaefer RJ, McCue ME. (2018). Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations. Front Genet, 9, 249. https://doi.org/10.3389/fgene.2018.00249

Publication

Frontiers in genetics
ISSN: 1664-8021
NlmUniqueID: 101560621
Country: Switzerland
Language: English
Volume: 9
Pages: 249

Researcher Affiliations

Avila, Felipe
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.
Mickelson, James R
  • Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.
Schaefer, Robert J
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.
McCue, Molly E
  • Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.

Grant Funding

  • K08 AR055713 / NIAMS NIH HHS

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