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 F. Bailey


The present research incorporated molecular genetic methods to 1) investigate the genetic basis of Juvenile Onset Lordosis or Swayback in the American Saddlebred horses; and 2) conduct a population genetic study to compare the Persian Kurdish, Persian Arabian and American Thoroughbred horse populations.

Juvenile-onset lordosis, or swayback, is a condition in horses where the conformational topline back curvature drops significantly within the first two years of life. The trait has a higher prevalence in Saddlebreds (5%). Prior research on them quantified the trait using a Measurement of Back Contour (MBC), defining an MBC of >7.0 centimeters as swayback, and8.0) MBC horses suggested a single recessive variant on chromosome20 to be associated with the trait. The present research aimed to find the causal mutation on chr20 using Whole-Genome Sequencing, testing a hypothesis that a single recessive variant on chr20 causes high-MBC. Eleven Saddlebreds were Whole-Genome Sequenced in two experiments. Experiment1 involved 3 high-MBC horses and 3 low-MBC horses with various haplotype structures on chr20. No variants were found on chr20 to support the hypothesis, suggesting more than one major variant to be involved in swayback. Re-evaluation of the association on chr20 was performed via genotyping for tag markers on a chr20 haplotype in 34 high-MBC versus 75 low-MBC Saddlebreds, where a chi-square comparison confirmed that chr20 has a significant impact on high-MBC and that the earlier GWAS association was not a statistical artifact.

We then evaluated all the genomic variation in the target region of chr20:41,000,000-44,000,000 to identify the best candidate to influence high-MBC in Saddlebreds. A total of 9,691 variant loci were detected that make 21,463 transcript variations. Of these, 599 made coding sequence variations, including 315 synonymous, 250 missense, 14 frameshift, 9 in-frame deletion, 7 in-frame insertion, and 2 splice-donor and 2 start-loss variants. The strongest candidate seems to be a frameshift deletion of 7bp in the exon 1 of the MDFI gene, at 20:41873061-41873068. MDFI-knockout mice show defects in the formation of thoracic vertebrae and ribs, which restrains fusion of the spinous processes.

The last part of the dissertation research is about a study that aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. The Kurdish horses were generally distinguished from the Persian Arabian and Thoroughbred samples by all analyses including Principal Component Analyses, cluster analyses and calculation of pairwise FST. These results together identify the Kurdish horse population as a unique, uniform genetic structure.

Digital Object Identifier (DOI)

Funding Information

American Saddlebred Horse Association funded the research project, 2018

Geoffrey Hughes foundation provided funding to support graduate studies, 2017

VCF_ASB_20_41_44.xlsx (583 kB)
Variant genotypes of the whole genome sequenced animals for the target region chr20:41M-44M