Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

被引:52
作者
Cai, Yudong [1 ]
Fu, Weiwei [1 ]
Cai, Dawei [2 ]
Heller, Rasmus [3 ]
Zheng, Zhuqing [1 ]
Wen, Jia [1 ]
Li, Hui [1 ,4 ]
Wang, Xiaolong [1 ]
Alshawi, Akil [5 ,6 ]
Sun, Zhouyong [7 ]
Zhu, Siqi [2 ]
Wang, Juan [8 ]
Yang, Miaomiao [7 ]
Hu, Songmei [7 ]
Li, Yan [1 ]
Yang, Zhirui [1 ]
Gong, Mian [1 ]
Hou, Yunan [1 ]
Lan, Tianming [9 ,10 ]
Wu, Kui [11 ,12 ]
Chen, Yulin [1 ]
Jiang, Yu [1 ]
Wang, Xihong [1 ]
机构
[1] Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling, Shaanxi, Peoples R China
[2] Jilin Univ, Res Ctr Chinese Frontier Archaeol, Changchun, Peoples R China
[3] Univ Copenhagen, Dept Biol, Sect Computat & RNA Biol, Copenhagen, Denmark
[4] Guangxi Univ, State Key Lab Conservat & Utilizat Subtrop Agrobi, Nanning, Peoples R China
[5] Univ Nottingham, Fac Med & Hlth Sci, Sch Life Sci, Nottingham, England
[6] Univ Baghdad, Coll Vet Med, Dept Internal & Prevent Med, Iraqi Minist Higher Educ & Sci Res, Baghdad, Iraq
[7] Shaanxi Acad Archaeol, Xian, Peoples R China
[8] Henan Prov Inst Cultural Heritage & Archaeol, Zhengzhou, Peoples R China
[9] BGI Shenzhen, Build 11, Shenzhen, Peoples R China
[10] Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, Copenhagen, Denmark
[11] BGI Shenzhen, China Natl GeneBank Shenzhen, Shenzhen, Peoples R China
[12] BGI Shenzhen, Canc Inst, BGI Res, Shenzhen, Peoples R China
基金
中国国家自然科学基金;
关键词
Chinese goats; ancient DNA; population genomics; adaptation; FGF5; EDA2R; FGF5;
D O I
10.1093/molbev/msaa103
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.
引用
收藏
页码:2099 / 2109
页数:11
相关论文
共 51 条
  • [1] Convergent genomic signatures of domestication in sheep and goats
    Alberto, Florian J.
    Boyer, Frederic
    Orozco-terWengel, Pablo
    Streeter, Ian
    Servin, Bertrand
    de Villemereuil, Pierre
    Benjelloun, Badr
    Librado, Pablo
    Biscarini, Filippo
    Colli, Licia
    Barbato, Mario
    Zamani, Wahid
    Alberti, Adriana
    Engelen, Stefan
    Stella, Alessandra
    Joost, Stephane
    Ajmone-Marsan, Paolo
    Negrini, Riccardo
    Orlando, Ludovic
    Rezaei, Hamid Reza
    Naderi, Saeid
    Clarke, Laura
    Flicek, Paul
    Wincker, Patrick
    Coissac, Eric
    Kijas, James
    Tosser-Klopp, Gwenola
    Chikhi, Abdelkader
    Bruford, Michael W.
    Taberlet, Pierre
    Pompanon, Francois
    [J]. NATURE COMMUNICATIONS, 2018, 9
  • [2] Allen J. A., 1877, Radical Review, Vi, P108
  • [3] Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
    Bickhart, Derek M.
    Rosen, Benjamin D.
    Koren, Sergey
    Sayre, Brian L.
    Hastie, Alex R.
    Chan, Saki
    Lee, Joyce
    Lam, Ernest T.
    Liachko, Ivan
    Sullivan, Shawn T.
    Burton, Joshua N.
    Huson, Heather J.
    Nystrom, John C.
    Kelley, Christy M.
    Hutchison, Jana L.
    Zhou, Yang
    Sun, Jiajie
    Crisa, Alessandra
    de Leon, F. Abel Ponce
    Schwartz, John C.
    Hammond, John A.
    Waldbieser, Geoffrey C.
    Schroeder, Steven G.
    Liu, George E.
    Dunham, Maitreya J.
    Shendure, Jay
    Sonstegard, Tad S.
    Phillippy, Adam M.
    Van Tassell, Curtis P.
    Smith, Timothy P. L.
    [J]. NATURE GENETICS, 2017, 49 (04) : 643 - +
  • [4] Edar signaling in the control of hair follicle development
    Botchkarev, VA
    Fessing, MY
    [J]. JOURNAL OF INVESTIGATIVE DERMATOLOGY SYMPOSIUM PROCEEDINGS, 2005, 10 (03) : 247 - 251
  • [5] The UCSC Genome Browser database: 2018 update
    Casper, Jonathan
    Zweig, Ann S.
    Villarreal, Chris
    Tyner, Cath
    Speir, Matthew L.
    Rosenbloom, Kate R.
    Raney, Brian J.
    Lee, Christopher M.
    Lee, Brian T.
    Karolchik, Donna
    Hinrichs, Angie S.
    Haeussler, Maximilian
    Guruvadoo, Luvina
    Gonzalez, Jairo Navarro
    Gibson, David
    Fiddes, Ian T.
    Eisenhart, Christopher
    Diekhans, Mark
    Clawson, Hiram
    Barber, Galt P.
    Armstrong, Joel
    Haussler, David
    Kuhn, Robert M.
    Kent, W. James
    [J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) : D762 - D769
  • [6] Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia
    Chen, Ningbo
    Cai, Yudong
    Chen, Qiuming
    Li, Ran
    Wang, Kun
    Huang, Yongzhen
    Hu, Songmei
    Huang, Shisheng
    Zhang, Hucai
    Zheng, Zhuqing
    Song, Weining
    Ma, Zhijie
    Ma, Yun
    Dang, Ruihua
    Zhang, Zijing
    Xu, Lei
    Jia, Yutang
    Liu, Shanzhai
    Yue, Xiangpeng
    Deng, Weidong
    Zhang, Xiaoming
    Sun, Zhouyong
    Lan, Xianyong
    Han, Jianlin
    Chen, Hong
    Bradley, Daniel G.
    Jiang, Yu
    Le, Chuzhao
    [J]. NATURE COMMUNICATIONS, 2018, 9
  • [7] Mitochondrial diversity and phylogeographic structure of Chinese domestic goats
    Chen, SY
    Su, YH
    Wu, SF
    Sha, T
    Zhang, YP
    [J]. MOLECULAR PHYLOGENETICS AND EVOLUTION, 2005, 37 (03) : 804 - 814
  • [8] DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
    Cornuet, Jean-Marie
    Pudlo, Pierre
    Veyssier, Julien
    Dehne-Garcia, Alexandre
    Gautier, Mathieu
    Leblois, Raphael
    Marin, Jean-Michel
    Estoup, Arnaud
    [J]. BIOINFORMATICS, 2014, 30 (08) : 1187 - 1189
  • [9] Ancient goat genomes reveal mosaic domestication in the Fertile Crescent
    Daly, Kevin G.
    Delser, Pierpaolo Maisano
    Mullin, Victoria E.
    Scheu, Amelie
    Mattiangeli, Valeria
    Teasdale, Matthew D.
    Hare, Andrew J.
    Burger, Joachim
    Verdugo, Marta Pereira
    Collins, Matthew J.
    Kehati, Ron
    Erek, Cevdet Merih
    Bar-Oz, Guy
    Pompanon, Francois
    Cumer, Tristan
    Cakirlar, Canan
    Mohaseb, Azadeh Fatemeh
    Decruyenaere, Delphine
    Davoudi, Hossein
    Cevik, Ozlem
    Rollefson, Gary
    Vigne, Jean-Denis
    Khazaeli, Roya
    Fathi, Homa
    Doost, Sanaz Beizaee
    Sorkhani, Roghayeh Rahimi
    Vahdati, Ali Akbar
    Sauer, Eberhard W.
    Kharanaghi, Hossein Azizi
    Maziar, Sepideh
    Gasparian, Boris
    Pinhasi, Ron
    Martin, Louise
    Orton, David
    Arbuckle, Benjamin S.
    Benecke, Norbert
    Manica, Andrea
    Horwitz, Liora Kolska
    Mashkour, Marjan
    Bradley, Daniel G.
    [J]. SCIENCE, 2018, 361 (6397) : 85 - 87
  • [10] The variant call format and VCFtools
    Danecek, Petr
    Auton, Adam
    Abecasis, Goncalo
    Albers, Cornelis A.
    Banks, Eric
    DePristo, Mark A.
    Handsaker, Robert E.
    Lunter, Gerton
    Marth, Gabor T.
    Sherry, Stephen T.
    McVean, Gilean
    Durbin, Richard
    [J]. BIOINFORMATICS, 2011, 27 (15) : 2156 - 2158