Genome-wide association analyses of equine metabolic syndrome phenotypes in welsh ponies and morgan horses

Elaine Norton, Nichol Schultz, Ray Geor, Dianne McFarlane, James Mickelson, Molly McCue

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Equine metabolic syndrome (EMS) is a complex trait for which few genetic studies have been published. Our study objectives were to perform within breed genome-wide association analyses (GWA) to identify associated loci in two high-risk breeds, coupled with meta-analysis to identify shared and unique loci between breeds. GWA for 12 EMS traits identified 303 and 142 associated genomic regions in 264 Welsh ponies and 286 Morgan horses, respectively. Meta-analysis demonstrated that 65 GWA regions were shared across breeds. Region boundaries were defined based on a fixed-size or the breakdown of linkage disequilibrium, and prioritized if they were: shared between breeds or across traits (high priority), identified in a single GWA cohort (medium priority), or shared across traits with no SNPs reaching genome-wide significance (low priority), resulting in 56 high, 26 medium, and seven low priority regions including 1853 candidate genes in the Welsh ponies; and 39 high, eight medium, and nine low priority regions including 1167 candidate genes in the Morgans. The prioritized regions contained protein-coding genes which were functionally enriched for pathways associated with inflammation, glucose metabolism, or lipid metabolism. These data demonstrate that EMS is a polygenic trait with breed-specific risk alleles as well as those shared across breeds.

Original languageEnglish (US)
Article number893
Issue number11
StatePublished - Nov 2019

Bibliographical note

Funding Information:
Funding: This research was funded by Foundation for the National Institute of Health, grant number T32OD010996; the Morris Animal Foundation, grant number D14EQ-033, Morris Animal Foundation doctoral fellowship, award number D17EQ-402; and the National Institute of Food and Agriculture, grant number 2009-55205-052542012-67015-19432.

Publisher Copyright:
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.


  • EMS
  • Fat metabolism
  • Genetic risk factors
  • Genetics
  • Genome-wide association analysis
  • Horses
  • Insulin dysregulation


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