BACKGROUND: Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait.
RESULTS: A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10− 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10− 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder.
CONCLUSIONS: This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.
Digital Object Identifier (DOI)
This work was funded by the Provost Undergraduate Fellowship at the Undergraduate Research Center, the College of Agriculture and Environmental Sciences, and the School of Veterinary Medicine at the University of California, Davis. This project was supported in part by the UC-Davis Center for Equine Health (17-24R and 16–12), with additional funds provided by the State of California Pari-Mutuel Fund and contributions by private donors. Funding from the Morris Animal Foundation (D16EQ-820) also helped to support this project.
This work was further supported by USDA NIFA-AFRI Project 2017–67015-26296: Tools to Link Phenotype to Genotype in the Horse, The American Quarter Horse Association, and a University of Minnesota Multistate grant. Salary support for SDA was provided by an American College of Veterinary Internal Medicine Foundation fellowship, by a T32 Institutional Training Grant in Comparative Medicine and Pathology (5T320D010993–12), and by the 2019 Elaine and Bertram Klein Development Award.
A portion of the datasets generated and/or analyzed during the current study are not publicly available as they are still being investigated for another related project but are available from the corresponding author on reasonable request. The remaining datasets generated and/or analyzed during the current study are available in the European Variation Archive (PRJEB34362: https://www.ebi.ac.uk/ena/browser/view/PRJEB34362, and PRJEB36380: https://www.ebi.ac.uk/ena/browser/view/PRJEB36380).
Hisey, E. A.; Hermans, H.; Lounsberry, Z. T.; Avila, F.; Grahn, R. A.; Knickelbein, K. E.; Duward-Akhurst, S. A.; McCue, M. E.; Kalbfleisch, Ted S.; Lassaline, M. E.; Back, W.; and Bellone, R. R., "Whole Genome Sequencing Identified a 16 Kilobase Deletion on ECA13 Associated with Distichiasis in Friesian Horses" (2020). Veterinary Science Faculty Publications. 51.