Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health
Abstract Background Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of s...
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BMC
2023-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09116-8 |
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| author | Haige Han Imtiaz A. S. Randhawa David E. MacHugh Beatrice A. McGivney Lisa M. Katz Manglai Dugarjaviin Emmeline W. Hill |
| author_facet | Haige Han Imtiaz A. S. Randhawa David E. MacHugh Beatrice A. McGivney Lisa M. Katz Manglai Dugarjaviin Emmeline W. Hill |
| author_sort | Haige Han |
| collection | DOAJ |
| description | Abstract Background Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. Results We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. Conclusions Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified. |
| first_indexed | 2024-04-10T21:04:14Z |
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| id | doaj.art-66be932713404468a9b7d822d2b4b60e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-10T21:04:14Z |
| publishDate | 2023-01-01 |
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| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-66be932713404468a9b7d822d2b4b60e2023-01-22T12:05:33ZengBMCBMC Genomics1471-21642023-01-0124111110.1186/s12864-023-09116-8Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof healthHaige Han0Imtiaz A. S. Randhawa1David E. MacHugh2Beatrice A. McGivney3Lisa M. Katz4Manglai Dugarjaviin5Emmeline W. Hill6Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Centre, Inner Mongolia Agricultural UniversityAnimal Genetics Laboratory, School of Veterinary Science, University of QueenslandUCD School of Agriculture and Food Science, University College DublinPlusvital Ltd, The HighlineUCD School of Veterinary Medicine, University College DublinInner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Centre, Inner Mongolia Agricultural UniversityUCD School of Agriculture and Food Science, University College DublinAbstract Background Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. Results We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. Conclusions Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.https://doi.org/10.1186/s12864-023-09116-8Chinese Mongolian horseSelection signaturesHoof healthRegional adaptation |
| spellingShingle | Haige Han Imtiaz A. S. Randhawa David E. MacHugh Beatrice A. McGivney Lisa M. Katz Manglai Dugarjaviin Emmeline W. Hill Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health BMC Genomics Chinese Mongolian horse Selection signatures Hoof health Regional adaptation |
| title | Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health |
| title_full | Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health |
| title_fullStr | Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health |
| title_full_unstemmed | Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health |
| title_short | Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health |
| title_sort | selection signatures for local and regional adaptation in chinese mongolian horse breeds reveal candidate genes for hoof health |
| topic | Chinese Mongolian horse Selection signatures Hoof health Regional adaptation |
| url | https://doi.org/10.1186/s12864-023-09116-8 |
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