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Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10684552/ https://www.ncbi.nlm.nih.gov/pubmed/38016956 http://dx.doi.org/10.1038/s41467-023-43626-z |
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author | Chen, Ningbo Xia, Xiaoting Hanif, Quratulain Zhang, Fengwei Dang, Ruihua Huang, Bizhi Lyu, Yang Luo, Xiaoyu Zhang, Hucai Yan, Huixuan Wang, Shikang Wang, Fuwen Chen, Jialei Guan, Xiwen Liu, Yangkai Li, Shuang Jin, Liangliang Wang, Pengfei Sun, Luyang Zhang, Jicai Liu, Jianyong Qu, Kaixing Cao, Yanhong Sun, Junli Liao, Yuying Xiao, Zhengzhong Cai, Ming Mu, Lan Siddiki, Amam Zonaed Asif, Muhammad Mansoor, Shahid Babar, Masroor Ellahi Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, Neena Amatya Terefe, Endashaw Belay, Gurja Tijjani, Abdulfatai Zegeye, Tsadkan Gebre, Mebrate Genet Ma, Yun Wang, Yu Huang, Yongzhen Lan, Xianyong Chen, Hong Migliore, Nicola Rambaldi Colombo, Giulia Semino, Ornella Achilli, Alessandro Sinding, Mikkel-Holger S. Lenstra, Johannes A. Cheng, Haijian Lu, Wenfa Hanotte, Olivier Han, Jianlin Jiang, Yu Lei, Chuzhao |
author_facet | Chen, Ningbo Xia, Xiaoting Hanif, Quratulain Zhang, Fengwei Dang, Ruihua Huang, Bizhi Lyu, Yang Luo, Xiaoyu Zhang, Hucai Yan, Huixuan Wang, Shikang Wang, Fuwen Chen, Jialei Guan, Xiwen Liu, Yangkai Li, Shuang Jin, Liangliang Wang, Pengfei Sun, Luyang Zhang, Jicai Liu, Jianyong Qu, Kaixing Cao, Yanhong Sun, Junli Liao, Yuying Xiao, Zhengzhong Cai, Ming Mu, Lan Siddiki, Amam Zonaed Asif, Muhammad Mansoor, Shahid Babar, Masroor Ellahi Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, Neena Amatya Terefe, Endashaw Belay, Gurja Tijjani, Abdulfatai Zegeye, Tsadkan Gebre, Mebrate Genet Ma, Yun Wang, Yu Huang, Yongzhen Lan, Xianyong Chen, Hong Migliore, Nicola Rambaldi Colombo, Giulia Semino, Ornella Achilli, Alessandro Sinding, Mikkel-Holger S. Lenstra, Johannes A. Cheng, Haijian Lu, Wenfa Hanotte, Olivier Han, Jianlin Jiang, Yu Lei, Chuzhao |
author_sort | Chen, Ningbo |
collection | PubMed |
description | Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle. |
format | Online Article Text |
id | pubmed-10684552 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-106845522023-11-30 Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing Chen, Ningbo Xia, Xiaoting Hanif, Quratulain Zhang, Fengwei Dang, Ruihua Huang, Bizhi Lyu, Yang Luo, Xiaoyu Zhang, Hucai Yan, Huixuan Wang, Shikang Wang, Fuwen Chen, Jialei Guan, Xiwen Liu, Yangkai Li, Shuang Jin, Liangliang Wang, Pengfei Sun, Luyang Zhang, Jicai Liu, Jianyong Qu, Kaixing Cao, Yanhong Sun, Junli Liao, Yuying Xiao, Zhengzhong Cai, Ming Mu, Lan Siddiki, Amam Zonaed Asif, Muhammad Mansoor, Shahid Babar, Masroor Ellahi Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, Neena Amatya Terefe, Endashaw Belay, Gurja Tijjani, Abdulfatai Zegeye, Tsadkan Gebre, Mebrate Genet Ma, Yun Wang, Yu Huang, Yongzhen Lan, Xianyong Chen, Hong Migliore, Nicola Rambaldi Colombo, Giulia Semino, Ornella Achilli, Alessandro Sinding, Mikkel-Holger S. Lenstra, Johannes A. Cheng, Haijian Lu, Wenfa Hanotte, Olivier Han, Jianlin Jiang, Yu Lei, Chuzhao Nat Commun Article Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle. Nature Publishing Group UK 2023-11-28 /pmc/articles/PMC10684552/ /pubmed/38016956 http://dx.doi.org/10.1038/s41467-023-43626-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Chen, Ningbo Xia, Xiaoting Hanif, Quratulain Zhang, Fengwei Dang, Ruihua Huang, Bizhi Lyu, Yang Luo, Xiaoyu Zhang, Hucai Yan, Huixuan Wang, Shikang Wang, Fuwen Chen, Jialei Guan, Xiwen Liu, Yangkai Li, Shuang Jin, Liangliang Wang, Pengfei Sun, Luyang Zhang, Jicai Liu, Jianyong Qu, Kaixing Cao, Yanhong Sun, Junli Liao, Yuying Xiao, Zhengzhong Cai, Ming Mu, Lan Siddiki, Amam Zonaed Asif, Muhammad Mansoor, Shahid Babar, Masroor Ellahi Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, Neena Amatya Terefe, Endashaw Belay, Gurja Tijjani, Abdulfatai Zegeye, Tsadkan Gebre, Mebrate Genet Ma, Yun Wang, Yu Huang, Yongzhen Lan, Xianyong Chen, Hong Migliore, Nicola Rambaldi Colombo, Giulia Semino, Ornella Achilli, Alessandro Sinding, Mikkel-Holger S. Lenstra, Johannes A. Cheng, Haijian Lu, Wenfa Hanotte, Olivier Han, Jianlin Jiang, Yu Lei, Chuzhao Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title_full | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title_fullStr | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title_full_unstemmed | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title_short | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
title_sort | global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10684552/ https://www.ncbi.nlm.nih.gov/pubmed/38016956 http://dx.doi.org/10.1038/s41467-023-43626-z |
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