Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau
Abstract Background On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestication, dispersal route, and the divergence of domestic yaks f...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | BMC Evolutionary Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12862-020-01702-8 |
| _version_ | 1818353475629613056 |
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| author | Zhi-xin Chai Jin-wei Xin Cheng-fu Zhang Dawayangla Luosang Qiang Zhang Pingcuozhandui Chao Li Yong Zhu Han-wen Cao Hui Wang Jian-lin Han Qiu-mei Ji Jin-cheng Zhong |
| author_facet | Zhi-xin Chai Jin-wei Xin Cheng-fu Zhang Dawayangla Luosang Qiang Zhang Pingcuozhandui Chao Li Yong Zhu Han-wen Cao Hui Wang Jian-lin Han Qiu-mei Ji Jin-cheng Zhong |
| author_sort | Zhi-xin Chai |
| collection | DOAJ |
| description | Abstract Background On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestication, dispersal route, and the divergence of domestic yaks from different areas are poorly understood. Results Here, we resequenced the genome of 91 domestic yak individuals from 31 populations and 1 wild yaks throughout China. Using a population genomics approach, we observed considerable genetic variation. Phylogenetic analysis suggested that the earliest domestications of yak occurred in the south-eastern QTP, followed by dispersal to the west QTP and northeast to SiChuang, Gansu, and Qinghai by two routes. Interestingly, we also found potential associations between the distribution of some breeds and historical trade routes such as the Silk Road and Tang-Tibet Ancient Road. Selective analysis identified 11 genes showing differentiation between domesticated and wild yaks and the potentially positively selected genes in each group were identified and compared among domesticated groups. We also detected an unbalanced pattern of introgression among domestic yak, wild yak, and Tibetan cattle. Conclusions Our research revealed population genetic evidence for three groups of domestic yaks. In addition to providing genomic evidence for the domestication history of yaks, we identified potential selected genes and introgression, which provide a theoretical basis and resources for the selective breeding of superior characters and high-quality yak. |
| first_indexed | 2024-12-13T19:10:07Z |
| format | Article |
| id | doaj.art-4184cd733cc8470297b96e9c458fe4eb |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-13T19:10:07Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-4184cd733cc8470297b96e9c458fe4eb2022-12-21T23:34:26ZengBMCBMC Evolutionary Biology1471-21482020-10-0120111010.1186/s12862-020-01702-8Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet PlateauZhi-xin Chai0Jin-wei Xin1Cheng-fu Zhang2Dawayangla3Luosang4Qiang Zhang5Pingcuozhandui6Chao Li7Yong Zhu8Han-wen Cao9Hui Wang10Jian-lin Han11Qiu-mei Ji12Jin-cheng Zhong13Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu UniversityState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu UniversityCAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS)State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry SciencesKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu UniversityAbstract Background On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestication, dispersal route, and the divergence of domestic yaks from different areas are poorly understood. Results Here, we resequenced the genome of 91 domestic yak individuals from 31 populations and 1 wild yaks throughout China. Using a population genomics approach, we observed considerable genetic variation. Phylogenetic analysis suggested that the earliest domestications of yak occurred in the south-eastern QTP, followed by dispersal to the west QTP and northeast to SiChuang, Gansu, and Qinghai by two routes. Interestingly, we also found potential associations between the distribution of some breeds and historical trade routes such as the Silk Road and Tang-Tibet Ancient Road. Selective analysis identified 11 genes showing differentiation between domesticated and wild yaks and the potentially positively selected genes in each group were identified and compared among domesticated groups. We also detected an unbalanced pattern of introgression among domestic yak, wild yak, and Tibetan cattle. Conclusions Our research revealed population genetic evidence for three groups of domestic yaks. In addition to providing genomic evidence for the domestication history of yaks, we identified potential selected genes and introgression, which provide a theoretical basis and resources for the selective breeding of superior characters and high-quality yak.http://link.springer.com/article/10.1186/s12862-020-01702-8DomesticationPlateau adaptabilityGene exchangeBovidaeHybridsSelective |
| spellingShingle | Zhi-xin Chai Jin-wei Xin Cheng-fu Zhang Dawayangla Luosang Qiang Zhang Pingcuozhandui Chao Li Yong Zhu Han-wen Cao Hui Wang Jian-lin Han Qiu-mei Ji Jin-cheng Zhong Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau BMC Evolutionary Biology Domestication Plateau adaptability Gene exchange Bovidae Hybrids Selective |
| title | Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau |
| title_full | Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau |
| title_fullStr | Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau |
| title_full_unstemmed | Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau |
| title_short | Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau |
| title_sort | whole genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the qinghai tibet plateau |
| topic | Domestication Plateau adaptability Gene exchange Bovidae Hybrids Selective |
| url | http://link.springer.com/article/10.1186/s12862-020-01702-8 |
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