Author ORCID Identifier

Date Available


Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation


Agriculture, Food and Environment


Veterinary Science

First Advisor

Dr. Ernest Bailey


This work consists of studies on dwarfism in Miniature horses and a study on breakdowns in Thoroughbreds in relation to gene aggrecan. A correction of the description and designation of D3 dwarf variant in aggrecan (ACAN) from the master’s thesis Chondrodysplasia-like dwarfism in the Miniature horse (2013). Commercial sequencing showed previous sequencing reads presented an artifact and not a single base deletion. Analysis showed a single base missense mutation in exon 8 identified as D3* was the actual cause. Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses by Eberth et al. (2018), corrected the error from the 2013 thesis.

An investigation was conducted of American Miniature horses for the presence of a dwarfism haplotype in ACAN previously discovered in Miniature horses of Brazil. Andrade et al. (2020) found a haplotype associated with a dwarf phenotype in the Miniature horses of Brazil, however the variant is non-causative. The Brazil Miniature population showed complete association of dwarfism to the haplotype. The American Miniature population did show a high correlation to dwarfism but did not show complete association of a dwarf phenotype and haplotype.

A study was conducted which focused on the genomic investigation for putative D5 dwarfism allele in Miniature horses. Eberth et al. (2018) described eight dwarf phenotype Miniature horses which only possessed 1 copy or no copies of the four mutations discovered. Whole genome sequencing was performed on two dwarfs possessing unknown genotypes. In silico analysis using PredictSNP showed 3 SNPs as likely deleterious to the function of the protein. A population of 464 Miniatures previously genotyped for dwarf variants D1, D2, D3, D4, and Brazil haplotype were tested with custom TaqMan assays designed for the three putative mutations. Variant g. 95258999 on Chromosome 1 shows independent segregation to dwarf variants D1, D2, D3, D4 and Brazil haplotype. We propose this variant is associated with a dwarf phenotype in the Miniature horse named D5.

An investigation was conducted into changes in breed standard head phenotypes and dwarfism in the Miniature horse. Facial structure of the Miniature horse has changed significantly due to the desires of breeders since the breed inception. Morphometric measurements using a landmark based method were obtained on 106 normal phenotype Miniature horses to compare size variance of specific facial features in relation to dwarf carrier status. Measurement results showed no correlation of specific facial feature size or shape to carrier state.

A study was conducted examining catastrophic injury in Thoroughbred training or racing and copy number variations in the ACAN VNTR region. A randomly selected group of 45 Thoroughbred horses and 17 horses that succumbed to injury on the racetrack were compared specifically for the sequence length of this region in aggrecan. Both groups presented significant variation in sequence length for this region of aggrecan. When the distribution of alleles between the two groups was compared, no significant differences were observed (P=0.699). This evidence suggests genetic variation for aggrecan and its ability to bind CS chains is not a major factor causing racetrack injury of Thoroughbred horses.

Digital Object Identifier (DOI)

Funding Information

This work was supported by Liza MacMillan through a private donation to the University of Kentucky Gluck Equine Research Center in 2019.