Novel variants in the HMGA2 gene are associated with withers height in Debao pony

Abstract The Debao pony is a well-known dwarf horse breed in China. HMGA2 gene (high-mobility group AT-hook 2)is regarded as one of important candidate genes regulating body height in horses. The aim of this study was to study the association between mutations in HMGA2gene and withers height in Debao ponies. The polymorphisms in all exons and partial introns of the HMGA2 gene were screened with sequencing across 180 Debao ponies. And the association between the DNA variants and withers height was analyzed. Seven genetic variants were identified in HMGA2 gene, including six novel variants. Among them, six mutations were located in two closed linked blocks. The three novel variants (In1-1, E5-1 and E5-2) in the 1th intron and the 5th exon and a known mutation (In1-2) had significant association with withers height in Debao ponies. These results suggest that the four variants have the potential to be used as genetic markers for dwarf horse breeding activities.