Recent selection and introgression facilitated high-altitude adaptation in cattle  

近期选择和耗牛渐渗共同促进黄牛对高原的适应性

作　　者：Yang Lyu Fuwen Wang Haijian Cheng Jing Han Ruihua Dang Xiaoting Xia Hui Wang Jincheng Zhong Johannes A.Lenstra Hucai Zhang Jianlin Han David E.MacHugh Ivica Medugorac Maulik Upadhyay Alexander SLeonard He Ding Xiaorui Yang Ming-Shan Wang Suolang Quji Basang Zhuzha Pubu Quzhen Silang Wangmu Nima Cangjue Da Wa Weidong Ma Jianyong Liu Jicai Zhang Bizhi Huang Xingshan Qi Fuqiang Li Yongzhen Huang Yun Ma Yu Wang Yuanpeng Gao Wenfa Lu Chuzhao Lei Ningbo Chen 吕阳;汪富文;成海建;韩静;党瑞华;夏小婷;王会;钟金城;Johannes ALenstra;张虎才;韩建林;David E.MacHugh;Ivica Medugorac;Maulik Upadhyay;Alexander S.Leonard;丁赫;杨筱芮;王明山;索朗曲吉;巴桑珠扎;普布曲珍;斯朗旺姆;尼玛仓决;达瓦;马伟东;刘建勇;张继才;黄必志;祁兴山;李付强;黄永震;马云;王禹;高元鹏;吕文发;雷初朝;陈宁博

机构地区：[1]Key Laboratory of Animal Genetics,Breeding and Reproduction of Shaanxi Province,College of Animal Science and Technology,Northwest A&F University,Yangling 712100,China [2]Key Laboratory of Animal Production,Product Quality,and Security,Ministry of Education,College of Animal Science and Technology,Jilin Agricultural University,Changchun 130118,China [3]Institute of Animal Science and Veterinary Medicine,Shandong Academy of Agricultural Sciences,Shandong Key Lab of Animal Disease Control and Breeding,Jinan 250000,China [4]College of Veterinary Medicine,Northwest A&F University,Yangling 712100,China [5]Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization,Sichuan Province and Ministry of Education,Southwest Minzu University,Chengdu 610000,China [6]Faculty of Veterinary Medicine,Utrecht University,Utrecht 3584 CM,The Netherlands [7]Institute for Ecological Research and Pollution Control of Plateau Lakes,School of Ecology and Environmental Science,Yunnan University,Kunming 650500,China [8]Southwest United Graduate School,Kunming 650500,China [9]Yazhouwan National Laboratory,Sanya 572024,China [10]CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources,Institute of Animal Science,Chinese Academy of Agriculture Sciences(CAAS),Beijing 100000,China [11]Animal Genomics Laboratory,UCD School of Agriculture and Food Science,University College Dublin,Dublin D04 V1W8,Ireland [12]UCD Conway Institute of Biomolecular and Biomedical Research,University College Dublin,Dublin D04 V1W8,Ireland [13]Population Genomics Group,Department of Veterinary Sciences,LMU Munich,Martinsried 82152,Germany [14]Animal Genomics,ETH Zurich,Universitaetstrasse 2,Zurich 8006,Switzerland [15]State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China [16]Institute of Animal Husbandry and Veterinary Science,Xizang Autonomous Region Academy of Agricultural and Animal

出　　处：《Science Bulletin》2024年第21期3415-3424,共10页科学通报（英文版）

基　　金：supported by the National Key R&D Program of China(2021YFD1200400 and 2021YFF1001000);the National Natural Science Foundation of China(32102523,32372854,31861143014,32260823,and 32172706);the Key Research and Development Program of Xizang Autonomous Region of China(XZ202301ZY0008N);the Yunnan Expert Workstations(202305AF150156),the China Agriculture Research System of MOF and MARA(CARS-37);the Postdoctoral Fellowship Program of CPSF(GZC20232149);the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry(202205AR070001);the Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements(2019ZG007);Finally,we thank the High-Performance Computing(HPC)Center of Northwest A&F University(NWAFU)and Hefei Advanced Computing Center for providing computing resources.

摘　　要：During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.

关 键 词：Tibetan cattle INTROGRESSION High-altitude adaptation Noncoding variant CIS-REGULATION 

分 类 号：S823[农业科学—畜牧学]