A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color.

Grilz-Seger, Gertrud; Reiter, Simone; Neuditschko, Markus; Wallner, Barbara; Rieder, Stefan; Leeb, Tosso; Jagannathan, Vidya; Mesarič, Matjaz; Cotman, Markus; Pausch, Hubert; Lindgren, Gabriella; Velie, Brandon; Horna, Michaela; Brem, Gottfried; Druml, Thomas (2020). A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color. Journal of equine veterinary science, 88, p. 102950. Elsevier 10.1016/j.jevs.2020.102950

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The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Research Foci > DermFocus
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

UniBE Contributor:

Leeb, Tosso and Jagannathan, Vidya

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture

ISSN:

0737-0806

Publisher:

Elsevier

Language:

English

Submitter:

Tosso Leeb

Date Deposited:

01 May 2020 11:47

Last Modified:

03 May 2020 02:42

Publisher DOI:

10.1016/j.jevs.2020.102950

PubMed ID:

32303326

Uncontrolled Keywords:

Coat color GWAS Genetic marker Horse KIT Roan

BORIS DOI:

10.7892/boris.143781

URI:

https://boris.unibe.ch/id/eprint/143781

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