Local Ancestry and Adaptive Introgression in Xiangnan Cattle
Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local env...
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2024-12-01
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| author | Huixuan Yan Jianbo Li Kunyu Zhang Hongfeng Duan Ao Sun Baizhong Zhang Fuqiang Li Ningbo Chen Chuzhao Lei Kangle Yi |
| author_facet | Huixuan Yan Jianbo Li Kunyu Zhang Hongfeng Duan Ao Sun Baizhong Zhang Fuqiang Li Ningbo Chen Chuzhao Lei Kangle Yi |
| author_sort | Huixuan Yan |
| collection | DOAJ |
| description | Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, <i>θ</i>π, <i>F</i><sub>ST</sub>, and XP-EHH methods, genes associated with immunity (<i>ITGB3</i>, <i>CD55</i>, <i>OTUD1</i>, and <i>PRLH</i>) and heat tolerance (<i>COX4I2</i>, <i>DNAJC18</i>, <i>DNAJC1</i>, <i>EIF2AK4</i>, and <i>ASIC2</i>) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources. |
| format | Article |
| id | doaj-art-2828d86920004486a522d3c8c21e562c |
| institution | DOAJ |
| issn | 2079-7737 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| spelling | doaj-art-2828d86920004486a522d3c8c21e562c2025-08-20T02:53:27ZengMDPI AGBiology2079-77372024-12-011312100010.3390/biology13121000Local Ancestry and Adaptive Introgression in Xiangnan CattleHuixuan Yan0Jianbo Li1Kunyu Zhang2Hongfeng Duan3Ao Sun4Baizhong Zhang5Fuqiang Li6Ningbo Chen7Chuzhao Lei8Kangle Yi9Hunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaHunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, ChinaHunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaHunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaHunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaHunan Tianhua Industrial Corporation Ltd., Lianyuan 417000, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, ChinaHunan Institute of Animal and Veterinary Science, Changsha 410131, ChinaExploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, <i>θ</i>π, <i>F</i><sub>ST</sub>, and XP-EHH methods, genes associated with immunity (<i>ITGB3</i>, <i>CD55</i>, <i>OTUD1</i>, and <i>PRLH</i>) and heat tolerance (<i>COX4I2</i>, <i>DNAJC18</i>, <i>DNAJC1</i>, <i>EIF2AK4</i>, and <i>ASIC2</i>) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources.https://www.mdpi.com/2079-7737/13/12/1000Xiangnan cattlepopulation structureselection signatureadaptive introgression |
| spellingShingle | Huixuan Yan Jianbo Li Kunyu Zhang Hongfeng Duan Ao Sun Baizhong Zhang Fuqiang Li Ningbo Chen Chuzhao Lei Kangle Yi Local Ancestry and Adaptive Introgression in Xiangnan Cattle Biology Xiangnan cattle population structure selection signature adaptive introgression |
| title | Local Ancestry and Adaptive Introgression in Xiangnan Cattle |
| title_full | Local Ancestry and Adaptive Introgression in Xiangnan Cattle |
| title_fullStr | Local Ancestry and Adaptive Introgression in Xiangnan Cattle |
| title_full_unstemmed | Local Ancestry and Adaptive Introgression in Xiangnan Cattle |
| title_short | Local Ancestry and Adaptive Introgression in Xiangnan Cattle |
| title_sort | local ancestry and adaptive introgression in xiangnan cattle |
| topic | Xiangnan cattle population structure selection signature adaptive introgression |
| url | https://www.mdpi.com/2079-7737/13/12/1000 |
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