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Background  Ponies are highly susceptible to metabolic derangements including hyperinsulinemia, insulin resistance, and adiposity.    Hypothesis/Objectives  Genetic loci affecting height in ponies have pleiotropic effects on metabolic pathways and increase the susceptibility to equine metabolic syndrome (EMS).    Animals  Two hundred ninety‐four Welsh ponies and 529 horses.    Methods  Retrospective study of horses phenotyped for metabolic traits. Correlations between height and metabolic traits were assessed by Pearson's correlation coefficients. Complementary genome‐wide analysis methods were used to identify a region of interest (ROI) for height and metabolic traits, determine the fraction of heritability contributed by the ROI, and identify candidate genes.    Results  There was an inverse relationship between height and baseline insulin (−0.26) in ponies. Genomic signature of selection and association analyses for both height and insulin identified the same ~1.3 megabase region on chromosome 6 that contained a shared ancestral haplotype between these traits. The ROI contributed ~40% of the heritability for height and ~20% of the heritability for insulin. High‐mobility group AT‐hook 2 was identified as a candidate gene, and Sanger sequencing detected a c.83G>A (p.G28E) variant associated with height in Shetland ponies. In our cohort of ponies, the A allele had a frequency of 0.76, was strongly correlated with height (−0.75), and was low to moderately correlated with metabolic traits including: insulin (0.32), insulin after an oral sugar test (0.25), non‐esterified fatty acids (0.19), and triglyceride (0.22) concentrations.    Conclusions and Clinical Importance  These data have important implications for identifying individuals at risk for EMS.

Evaluation of an HMGA2 variant for pleiotropic effects on height and metabolic traits in ponies