An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses
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—<i>ASIP</i> and <i>MC1R</i>. These genes direct the type of pigment produced, red pheomelanin (<...
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| Format: | Article |
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MDPI AG
2020-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/6/606 |
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| author | Laura J. Corbin Jessica Pope Jacqueline Sanson Douglas F. Antczak Donald Miller Raheleh Sadeghi Samantha A. Brooks |
| author_facet | Laura J. Corbin Jessica Pope Jacqueline Sanson Douglas F. Antczak Donald Miller Raheleh Sadeghi Samantha A. Brooks |
| author_sort | Laura J. Corbin |
| collection | DOAJ |
| description | 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—<i>ASIP</i> and <i>MC1R</i>. These genes direct the type of pigment produced, red pheomelanin (<i>MC1R</i>) or black eumelanin (<i>ASIP</i>), as well as the relative concentration and the temporal–spatial 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 <i>ASIP</i> gene (<i>p =</i> 9.76 × 10<sup>−15</sup>). This candidate region encompasses the distal 5′ end of the <i>ASIP</i> transcript (as predicted from other species) as well as the <i>RALY</i> 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 <i>ASIP</i> alleles, especially those in the 5′ regulatory region, improved understanding of this new <i>Shade</i> allele may have implications for health management in the horse. |
| first_indexed | 2024-03-10T19:29:11Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T19:29:11Z |
| publishDate | 2020-05-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-e6eb140425514397a9061ac8ea72c7f62023-11-20T02:17:21ZengMDPI AGGenes2073-44252020-05-0111660610.3390/genes11060606An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in HorsesLaura J. Corbin0Jessica Pope1Jacqueline Sanson2Douglas F. Antczak3Donald Miller4Raheleh Sadeghi5Samantha A. Brooks6Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UKBristol Veterinary School, University of Bristol, Bristol BS8 1QU, UKDepartment of Animal Sciences, University of Florida, Gainesville, FL 32610, USABaker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USABaker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USABaker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USADepartment of Animal Sciences, University of Florida, Gainesville, FL 32610, USANovel 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—<i>ASIP</i> and <i>MC1R</i>. These genes direct the type of pigment produced, red pheomelanin (<i>MC1R</i>) or black eumelanin (<i>ASIP</i>), as well as the relative concentration and the temporal–spatial 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 <i>ASIP</i> gene (<i>p =</i> 9.76 × 10<sup>−15</sup>). This candidate region encompasses the distal 5′ end of the <i>ASIP</i> transcript (as predicted from other species) as well as the <i>RALY</i> 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 <i>ASIP</i> alleles, especially those in the 5′ regulatory region, improved understanding of this new <i>Shade</i> allele may have implications for health management in the horse.https://www.mdpi.com/2073-4425/11/6/606horseequinebaycoat colourASIPgenome-wide association study |
| spellingShingle | Laura J. Corbin Jessica Pope Jacqueline Sanson Douglas F. Antczak Donald Miller Raheleh Sadeghi Samantha A. Brooks An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses Genes horse equine bay coat colour ASIP genome-wide association study |
| title | An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses |
| title_full | An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses |
| title_fullStr | An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses |
| title_full_unstemmed | An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses |
| title_short | An Independent Locus Upstream of <i>ASIP</i> Controls Variation in the Shade of the Bay Coat Colour in Horses |
| title_sort | independent locus upstream of i asip i controls variation in the shade of the bay coat colour in horses |
| topic | horse equine bay coat colour ASIP genome-wide association study |
| url | https://www.mdpi.com/2073-4425/11/6/606 |
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