{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T19:27:38Z","timestamp":1792006058247,"version":"4.4.0"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,5,30]],"date-time":"2020-05-30T00:00:00Z","timestamp":1590796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses\u2014ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal\u2013spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 \u00d7 10\u221215). This candidate region encompasses the distal 5\u2032 end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5\u2032 regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.<\/jats:p>","DOI":"10.3390\/genes11060606","type":"journal-article","created":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T09:19:27Z","timestamp":1591089567000},"page":"606","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4032-9500","authenticated-orcid":false,"given":"Laura J.","family":"Corbin","sequence":"first","affiliation":[{"name":"Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK"},{"name":"MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Pope","sequence":"additional","affiliation":[{"name":"Bristol Veterinary School, University of Bristol, Bristol BS8 1QU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline","family":"Sanson","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas F.","family":"Antczak","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald","family":"Miller","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raheleh","family":"Sadeghi","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4500-2689","authenticated-orcid":false,"given":"Samantha A.","family":"Brooks","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA"},{"name":"UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,5,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.2174\/1389202003351364","article-title":"Molecular Genetics of Pigmentation in Domestic Animals","volume":"1","author":"Klungland","year":"2000","journal-title":"Curr. 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