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Home / Equine Research Bank / BMC Genomics / Whole genome sequencing identified a 16 kilobase deletion on...
BMC genomics2020; 21(1); 848; doi: 10.1186/s12864-020-07265-8

Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses.

Abstract: 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.
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Publication Date: 2020-11-30 PubMed ID: 33256610PubMed Central: PMC7706231DOI: 10.1186/s12864-020-07265-8Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study on Friesian horses that discovered a genetic mutation associated with a breed-specific eye disorder named distichiasis, which causes abnormal eyelash growth and can affect vision.

Context and Relevance

  • The article is centered around distichiasis, a notable ocular disorder appearing predominantly in the Friesian horse breed which causes unusual eyelash growth originating from the eyelid’s Meibomian glands.
  • Anomalously grown eyelashes can lead to discomfort, long-lasting keratitis, and corneal ulceration. The resulting complications can include compromised vision due to corneal fibrosis, or even loss of the eye in case a secondary infection occurs.
  • In most cases, Friesian horses are affected and the breed is also associated with various inherited monogenic disorders. Hence, researchers hypothesized that distichiasis would follow a similar pattern of genetic inheritance.

Methodology and Results

  • A genome-wide association study was carried out using 14 affected horses and 38 healthy controls. The researchers used the Axiom 670 k Equine Genotyping array, with an additive single locus mixed linear model approach.
  • During the analysis, two locations on the horse genomes (locus on ECA5 and ECA13) were identified as potentially significant
  • Upon subsequent replication testing, only the locus on ECA13 held its significance.
  • Further analysis revealed a 371 kb run of homozygosity on ECA13 in most of the cases, indicating a recessive mode of inheritance of the disorder.

Identification of Deletion

  • The region of association on ECA13 was narrowed down to 163 kb using a haplotype analysis.
  • A subsequent whole-genome sequencing with 3 affected horses and 2 healthy controls identified a specific 16 kb deletion on ECA13. The data indicates this region has a tissue-specific regulatory role.
  • The deletion was found to be highly associated with distichiasis as 18 out of 19 cases were homozygous for it.

Implications

  • Deletion genotyping across various horse breeds showed the deletion mainly in Friesian horses, reinforcing that it could be causal for the disorder in this breed. The deletion was also found in some non-Friesians, but all were carriers, not affected by the disorder.
  • The study concludes by identifying a 16 kb deletion on ECA13 associated with distichiasis in Friesian horses. However, further investigation is required to establish the precise role of this deletion in normal and abnormal eyelash development and to explore the hypothesis of incomplete penetrance – that is, the possibility that not all horses with the deletion will display the disorder.

Cite This Article

APA
Hisey EA, Hermans H, Lounsberry ZT, Avila F, Grahn RA, Knickelbein KE, Duward-Akhurst SA, McCue ME, Kalbfleisch TS, Lassaline ME, Back W, Bellone RR. (2020). Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses. BMC Genomics, 21(1), 848. https://doi.org/10.1186/s12864-020-07265-8

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 848

Researcher Affiliations

Hisey, E A
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Hermans, H
  • Department of Clinical Sciences, Utrecht University, Yalelaan 112-114, NL-3584, CM, Utrecht, The Netherlands.
Lounsberry, Z T
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Avila, F
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Grahn, R A
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Knickelbein, K E
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
  • Veterinary Medical Teaching Hospital, University of California-Davis, Davis, CA, USA.
Duward-Akhurst, S A
  • Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA.
McCue, M E
  • Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA.
Kalbfleisch, T S
  • Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA.
Lassaline, M E
  • Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Back, W
  • Department of Clinical Sciences, Utrecht University, Yalelaan 112-114, NL-3584, CM, Utrecht, The Netherlands.
  • Department of Surgery and Anaesthesia of Domestic Animals, Ghent University, Merelbeke, Belgium.
Bellone, R R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA. rbellone@ucdavis.edu.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA. rbellone@ucdavis.edu.

MeSH Terms

  • Animals
  • Eyelid Diseases / genetics
  • Eyelid Diseases / veterinary
  • Eyelids / pathology
  • Genome-Wide Association Study
  • Haplotypes
  • Horse Diseases / genetics
  • Horses
  • Phenotype
  • Whole Genome Sequencing

Grant Funding

  • 16-12 / University of Califorina Davis Center for Equine Health
  • 5T320D010993-12 / NIH HHS
  • 2017-67015-26296 / National Institute of Food and Agriculture
  • T32 OD010993 / NIH HHS
  • N/A / University of California Davis
  • N/A / University of California Davis Provost Undergraduate Research Fellowship
  • D16EQ-820 / Morris Animal Foundation
  • 17-24R / University of California Davis Center for Equine Health

Conflict of Interest Statement

FA, RAG and RRB are affiliated with the Veterinary Genetics Laboratory, a laboratory offering diagnostic tests in horses.

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Citations

This article has been cited 9 times.
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