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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.

References

This article includes 54 references
  1. Weinberg WC, Goodman LV, George C, Morgan DL, Ledbetter S, Yuspa SH, Lichti U. Reconstitution of hair follicle development in vivo: determination of follicle formation, hair growth, and hair quality by dermal cells.. J Invest Dermatol 1993;100:229–236.
    doi: 10.1111/1523-1747.ep12468971pubmed: 8440892google scholar: lookup
  2. Paus R, Cotsarelis G. The biology of hair follicles.. N Engl J Med 1999;341:491–497.
    doi: 10.1056/NEJM199908123410706pubmed: 10441606google scholar: lookup
  3. Johnstone MA, Albert DM. Prostaglandin-induced hair growth.. Surv Ophthalmol 2002;47(Suppl):185–202.
    doi: 10.1016/S0039-6257(02)00307-7pubmed: 12204716google scholar: lookup
  4. Scheie HG, Yanoff M, Frayer WC. Carcinoma of sebaceous glands of the eyelid.. Arch Ophthalmol 1964;27:800–803.
    doi: 10.1001/archopht.1964.00970020802011pubmed: 14205440google scholar: lookup
  5. Scheie HG, Albert DM. Distichiasis and trichiasis: origin and management.. Am J Ophthalmol 1966;61:718–720.
    doi: 10.1016/0002-9394(66)91209-8pubmed: 5931268google scholar: lookup
  6. Alsuhaibani AH, Carter KD, Abràmoff MD, Nerad JA. Utility of meibography in the evaluation of Meibomian glands morphology in normal and diseased eyelids.. Saudi J Othalmol 2011;25:61–66.
    doi: 10.1016/j.sjopt.2010.10.005pmc: PMC3729445pubmed: 23960903google scholar: lookup
  7. O’Donnell BA, Collin JRO. Distichiasis: management with cryotherapy to the posterior lamella.. Br J Ophthalmol 1993;77:289–292.
    doi: 10.1136/bjo.77.5.289pmc: PMC504507pubmed: 8318465google scholar: lookup
  8. Alkatan HM, Galindo-Ferreiro A, Maktabi A, Galvez-Ruiz A, Schellini S. Congenital distichiasis: histopathological report of 3 cases.. Saudi J Othalmol 2017;31:165–168.
    doi: 10.1016/j.sjopt.2017.05.003pmc: PMC5569325pubmed: 28860915google scholar: lookup
  9. Patil BB, Bell R, Brice G, Jeffery S, Lymphoedema Research Group. Distichiasis without lymphoedema?. Eye 2004;18:1270–1272.
    doi: 10.1038/sj.eye.6701387pubmed: 15044942google scholar: lookup
  10. Galindo-Ferreiro A, Alkatan H, Maktabi A, Galvez-Ruiz A, Schellini S. A new surgical technique for congenital distichiasis.. Orbit 2017;37:87–90.
    doi: 10.1080/01676830.2017.1383454pubmed: 29058522google scholar: lookup
  11. Utter ME, Wotman KL. Distichiasis causing recurrent corneal ulceration in two Friesian horses.. Equine Vet Educ 2012;24:556–560.
    doi: 10.1111/j.2042-3292.2011.00336.xgoogle scholar: lookup
  12. Hermans H, Ensink JM. Treatment and long-term follow-up of distichiasis, with special reference to the Friesian horse: a case series.. Equine Vet J 2014;46:458–462.
    doi: 10.1111/evj.12157pubmed: 23927412google scholar: lookup
  13. Brooks BP, Dagenais SL, Nelson CC, Glynn MW, Caulder MS, Downs CA, Glover TW. Mutation of the FOXC2 gene in familial distichiasis.. J AAPOS 2003;7:354–357.
    doi: 10.1016/S1091-8531(03)00144-7pubmed: 14566319google scholar: lookup
  14. Zhang L, He J, Han B, Lu L, Fan J, Zhang H. Novel FOXC2 mutation in hereditary distichiasis impairs DNA-binding activity and transcriptional activation.. Int J Biol Sci 2016;12:1114–1120.
    doi: 10.7150/ijbs.13774pmc: PMC4997055pubmed: 27570485google scholar: lookup
  15. Halliwell WH. Surgical management of canine distichia.. J Am Vet Med Assoc 1967;171:275–277.
    pubmed: 6068021
  16. Schurink A, Shrestha M, Eriksson S, Bosse M, Bovenhuis H, Back W. The genomic makeup of nine horse populations sampled in the Netherlands.. Genes 2019;10:480.
    doi: 10.3390/genes10060480pmc: PMC6627704pubmed: 31242710google scholar: lookup
  17. Ducro BJ, Schurink A, Bastiaansen JWM, Boegheim IJM, van Steenbeek FG, Vos-Loohuis M. A nonsense mutation in B3GALNT2 is concordant with hydrocephalus in Friesian horses.. BMC Genomics 2015;16:761.
    doi: 10.1186/s12864-015-1936-zpmc: PMC4600337pubmed: 26452345google scholar: lookup
  18. Leegwater PA, Vos-Loohuis M, Ducro BJ, Boegheim IJ, van Steenbeek FG, Nijman IJ. Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7.. BMC Genomics 2016;17:839.
    doi: 10.1186/s12864-016-3186-0pmc: PMC5084406pubmed: 27793082google scholar: lookup
  19. Alberi C, Hisey E, Lassaline M, Atilano A, Kalbfleisch T, Stoppini R. Ruling out BGN variants as simple X-linked causative mutations for bilateral corneal stromal loss in Friesian horses.. Anim Genet 2018;49:656–657.
    doi: 10.1111/age.12726pubmed: 30246344google scholar: lookup
  20. Ploeg M, Gröne A, Saey V, de Bruijn CM, Back W, van Weeren PR. Esophageal dysfunction in Friesian horses: morphological features.. Vet Pathol 2014;52:1142–1147.
    doi: 10.1177/0300985814556780pubmed: 25367366google scholar: lookup
  21. Sevinga M, Barkema HW, Stryhn H, Hesselink JW. Retained placenta in Friesian mares: incidence, and potential risk factors with special emphasis on gestational length.. Theriogenol 2004;61:851–859.
    doi: 10.1016/S0093-691X(03)00260-7pubmed: 14757471google scholar: lookup
  22. Sipma KD, Cornillie P, Saulez MN, Stout TAE, Voorhout G, Back W. Phenotypic characteristics of hydrocephalus in stillborn Friesian foals.. Vet Pathol 2013;50:1037–1042.
    doi: 10.1177/0300985813488955pubmed: 23676552google scholar: lookup
  23. Ploeg M, Saey V, de Bruijn CM, Gröne A, Chiers K, van Loon G. Aortic rupture and aorto-pulmonary fistulation in the Friesian horse: characterisation of the clinical and gross post mortem findings in 24 cases.. Equine Vet J 2013;45:101–106.
    doi: 10.1111/j.2042-3306.2012.00580.xpubmed: 22607232google scholar: lookup
  24. Affolter VK. Chronic progressive lymphedema in draft horses.. Vet Clin Equine 2013;29:589–605.
    doi: 10.1016/j.cveq.2013.08.007pubmed: 24267677google scholar: lookup
  25. Xu H, Guan Y. Detecting local haplotype sharing and haplotype association.. Genetics 2014;197:823–838.
    doi: 10.1534/genetics.114.164814pmc: PMC4096364pubmed: 24812308google scholar: lookup
  26. Kalbfleisch TS, Rice ES, DePriest MS, Walenz BP, Hestand MS, Vermeesch J. Improved reference genome for the domestic horse increases assembly continuity and composition.. Commun Biol 2018;1:197.
    doi: 10.1038/s42003-018-0199-zpmc: PMC6240028pubmed: 30456315google scholar: lookup
  27. Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F. Generation of an equine biobank to be used for functional annotation of animal genomes project.. Anim Genet 2018;49(6):564–570.
    doi: 10.1111/age.12717pmc: PMC6264908pubmed: 30311254google scholar: lookup
  28. Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS. Functionally annotating regulatory elements in the equine genome using histone mark ChIP-Seq.. Genes 2020;11:3.
    doi: 10.3390/genes11010003pmc: PMC7017286pubmed: 31861495google scholar: lookup
  29. Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome.. Nature Biotechnol 2017;35:732–746.
    doi: 10.1038/nbt.3863pubmed: 28787426google scholar: lookup
  30. Mahon GAT, Cunningham EP. Inbreeding and the inheritance of fertility in the thoroughbred mare.. Livest Prod Sci 1982;9:743–754.
    doi: 10.1016/0301-6226(82)90021-5google scholar: lookup
  31. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfennig DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses.. J Hered 1983;74:394–399.
    doi: 10.1093/oxfordjournals.jhered.a109824google scholar: lookup
  32. Conant EK, Juras R, Cothran EG. A microsatellite analysis of five colonial Spanish horse populations of the southeastern United States.. Anim Genet 2011;43:53–62.
    doi: 10.1111/j.1365-2052.2011.02210.xpubmed: 22221025google scholar: lookup
  33. Yamamoto S, Fukumoto E, Yoshizaki K, Iwamoto T, Yamada A, Tanaka K. Platelet-derived growth factor receptor regulates salivary gland morphogenesis via fibroblast growth factor expression.. J Biol Chem 2008;283:23139–23149.
    doi: 10.1074/jbc.M710308200pubmed: 18559345google scholar: lookup
  34. Bellone RR, Liu J, Petersen JL, Mack M, Singer-Berk M, Drögemüller C. A missense mutation in damage-specific DNA binding protein 2 is a genetic risk factor for limbal squamous cell carcinoma in horses.. Int J Cancer 2017;2:342–353.
    doi: 10.1002/ijc.30744pubmed: 28425625google scholar: lookup
  35. FHANA Royal Friesian by KFPS. www.FHANA.com. Accessed 16 Oct 2018.
  36. Garbe JR, Da Y. Pedigraph: a software tool for the graphing and analysis of large complex pedigree. User manual Version 2.4.. Department of Animal Science, University of Minnesota. 2008.
  37. Social Science Statistics. https://www.socscistatistics.com/tests/mannwhitney/ 24 Jun 2019.
  38. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.. BMC Genomics 2017;18:565.
    doi: 10.1186/s12864-017-3943-8pmc: PMC5530493pubmed: 28750625google scholar: lookup
  39. Golden Helix: SNP and Variation Suite, version 8.s7.1. https://www.goldenhelix.com/products/SNP_Variation/index.html. Accessed 8 Oct 2018.
  40. Beeson SK, Schaefer RJ, Mason V, McCue ME. Robust re-mapping of equine SNP array coordinates to Eq쪳.. Anim Genet 2019;50(1):114–115.
    doi: 10.1111/age.12745pmc: PMC6349531pubmed: 30421446google scholar: lookup
  41. Li M, Yeung JMY, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.. Hum Genet 2012;131:747–756.
    doi: 10.1007/s00439-011-1118-2pmc: PMC3325408pubmed: 22143225google scholar: lookup
  42. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong S, Freimer NB. Variance component model to account for sample structure in genome-wide association studies.. Nat Genet 2010;42:348–354.
    doi: 10.1038/ng.548pmc: PMC3092069pubmed: 20208533google scholar: lookup
  43. San Millán RM, Martínez-Ballesteros I, Rementeria A, Garaizar J, Bikandi J. Online exercise for the design and simulation of PCR and PCR-RFLP experiments.. BMC Research Notes 2013.
    pmc: PMC4029544pubmed: 24314313doi: 10.1186/1756-0500-6-513google scholar: lookup
  44. Gabriel S, Ziaugra L, Tabbaa D. SNP genotyping using the Sequenom MassARRAY iPLEX platform.. Curr Protoc Hum Genet 2009;2:1–18.
    pubmed: 19170031
  45. Settles, M. GitHub. https://github.com/ibest/HTStream. Accessed 2 Nov 2018.
  46. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform.. Bioinformatics 2009;25:1754–1760.
    doi: 10.1093/bioinformatics/btp324pmc: PMC2705234pubmed: 19451168google scholar: lookup
  47. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing.. 2012.
  48. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N. The sequence alignment/map format and SAMtools.. Bioinformatics 2009;25:2078–2079.
    doi: 10.1093/bioinformatics/btp352pmc: PMC2723002pubmed: 19505943google scholar: lookup
  49. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.. Fly 2012;6:80–92.
    doi: 10.4161/fly.19695pmc: PMC3679285pubmed: 22728672google scholar: lookup
  50. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration.. Brief Bioinformatics 2013;14:178–192.
    doi: 10.1093/bib/bbs017pmc: PMC3603213pubmed: 22517427google scholar: lookup
  51. Layer RM, Chiang C, Quinlan AR, Hall I. M LUMPY: a probabilistic framework for structural variant discovery.. Genome Biol 2014;15:R84.
    doi: 10.1186/gb-2014-15-6-r84pmc: PMC4197822pubmed: 24970577google scholar: lookup
  52. BLAST. https://blast.ncbi.nlm.nih.gov/Blast.cgi#. Accessed 20 Feb 2019.
  53. Toonen RJ, Hughes S. Increased throughput for fragment analysis on ABI prism 377 automated sequencer using a membrane comb and STRand software.. Biotechniques 2001;31:1320–1324.
    pubmed: 11768661
  54. Handsaker RE, Korn JM, Nemesh J, McCarroll SA. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.. Nat Genet 2011;43:269–276.
    doi: 10.1038/ng.768pmc: PMC5094049pubmed: 21317889google scholar: lookup

Citations

This article has been cited 9 times.
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