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Open AccessArticle

Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses

1
Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
2
College of Sciences, Massey University, Palmerston North 4442, New Zealand
3
Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA
4
Veterinary Biomedical Sciences Department, University of Minnesota; St. Paul, MN 55108, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(11), 893; https://doi.org/10.3390/genes10110893
Received: 12 October 2019 / Revised: 31 October 2019 / Accepted: 1 November 2019 / Published: 6 November 2019
(This article belongs to the Special Issue Equine Genetics)
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. View Full-Text
Keywords: EMS; insulin dysregulation; fat metabolism; genetics; genetic risk factors; horses; genome-wide association analysis EMS; insulin dysregulation; fat metabolism; genetics; genetic risk factors; horses; genome-wide association analysis
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Norton, E.; Schultz, N.; Geor, R.; McFarlane, D.; Mickelson, J.; McCue, M. Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses. Genes 2019, 10, 893.

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