Origin and adaptation to high altitude of Tibetan semi-wild wheat

被引:146
作者
Guo, Weilong [1 ]
Xin, Mingming [1 ]
Wang, Zihao [1 ]
Yao, Yingyin [1 ]
Hu, Zhaorong [1 ]
Song, Wanjun [1 ]
Yu, Kuohai [1 ]
Chen, Yongming [1 ]
Wang, Xiaobo [1 ]
Guan, Panfeng [1 ]
Appels, Rudi [2 ,3 ]
Peng, Huiru [1 ]
Ni, Zhongfu [1 ]
Sun, Qixin [1 ]
机构
[1] China Agr Univ, Beijing Key Lab Crop Genet Improvement, Key Lab Crop Heterosis & Utilizat MOE, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China
[2] La Trobe Univ, Dept Econ Dev Jobs Transport & Resources, Ctr AgriBiosci, AgriBio, 5 Ring Rd, Bundoora, Vic 3083, Australia
[3] Univ Melbourne, FVAS, Grattan St, Parkville, Vic 3010, Australia
基金
中国国家自然科学基金;
关键词
BRITTLE RACHIS; GENOME; SEQUENCE; GENE; ALIGNMENT; IDENTIFICATION; PROTEIN; GENERATION; PREDICTION; DIVERSITY;
D O I
10.1038/s41467-020-18738-5
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces. We demonstrate that high-altitude environments can trigger extensive reshaping of wheat genomes, and also uncover that Tibetan wheat accessions accumulate high-altitude adapted haplotypes of related genes in response to harsh environmental constraints. Moreover, we find that Tibetan semi-wild wheat is a feral form of Tibetan landrace, and identify two associated loci, including a 0.8-Mb deletion region containing Brt1/2 homologs and a genomic region with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence to support the hypothesis that Tibetan semi-wild wheat is de-domesticated from local landraces, in response to high-altitude extremes. Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.
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页数:12
相关论文
共 80 条
[1]   Fast model-based estimation of ancestry in unrelated individuals [J].
Alexander, David H. ;
Novembre, John ;
Lange, Kenneth .
GENOME RESEARCH, 2009, 19 (09) :1655-1664
[2]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[3]  
[Anonymous], 2018, BMJ, V361, pk2475, DOI 10.1136/bmj.k2475
[4]   Wild emmer genome architecture and diversity elucidate wheat evolution and domestication [J].
Avni, Raz ;
Nave, Moran ;
Barad, Omer ;
Baruch, Kobi ;
Twardziok, Sven O. ;
Gundlach, Heidrun ;
Hale, Iago ;
Mascher, Martin ;
Spannagl, Manuel ;
Wiebe, Krystalee ;
Jordan, Katherine W. ;
Golan, Guy ;
Deek, Jasline ;
Ben-Zvi, Batsheva ;
Ben-Zvi, Gil ;
Himmelbach, Axel ;
MacLachlan, Ron P. ;
Sharpe, Andrew G. ;
Fritz, Allan ;
Ben-David, Roi ;
Budak, Hikmet ;
Fahima, Tzion ;
Korol, Abraham ;
Faris, Justin D. ;
Hernandez, Alvaro ;
Mikel, Mark A. ;
Levy, Avraham A. ;
Steffenson, Brian ;
Maccaferri, Marco ;
Tuberosa, Roberto ;
Cattivelli, Luigi ;
Faccioli, Primetta ;
Ceriotti, Aldo ;
Kashkush, Khalil ;
Pourkheirandish, Mohammad ;
Komatsuda, Takao ;
Eilam, Tamar ;
Sela, Hanan ;
Sharon, Amir ;
Ohad, Nir ;
Chamovitz, Daniel A. ;
Mayer, Klaus F. X. ;
Stein, Nils ;
Ronen, Gil ;
Peleg, Zvi ;
Pozniak, Curtis J. ;
Akhunov, Eduard D. ;
Distelfeld, Assaf .
SCIENCE, 2017, 357 (6346) :93-96
[5]   Genetic strategies for improving crop yields [J].
Bailey-Serres, Julia ;
Parker, Jane E. ;
Ainsworth, Elizabeth A. ;
Oldroyd, Giles E. D. ;
Schroeder, Julian I. .
NATURE, 2019, 575 (7781) :109-118
[6]   BamTools: a C++ API and toolkit for analyzing and managing BAM files [J].
Barnett, Derek W. ;
Garrison, Erik K. ;
Quinlan, Aaron R. ;
Stroemberg, Michael P. ;
Marth, Gabor T. .
BIOINFORMATICS, 2011, 27 (12) :1691-1692
[7]   The origins of wheat in China and potential pathways for its introduction: A review [J].
Betts, Alison ;
Jia, Peter Weiming ;
Dodson, John .
QUATERNARY INTERNATIONAL, 2014, 348 :158-168
[8]   GeneWise and genomewise [J].
Birney, E ;
Clamp, M ;
Durbin, R .
GENOME RESEARCH, 2004, 14 (05) :988-995
[9]   Trimmomatic: a flexible trimmer for Illumina sequence data [J].
Bolger, Anthony M. ;
Lohse, Marc ;
Usadel, Bjoern .
BIOINFORMATICS, 2014, 30 (15) :2114-2120
[10]   TASSEL: software for association mapping of complex traits in diverse samples [J].
Bradbury, Peter J. ;
Zhang, Zhiwu ;
Kroon, Dallas E. ;
Casstevens, Terry M. ;
Ramdoss, Yogesh ;
Buckler, Edward S. .
BIOINFORMATICS, 2007, 23 (19) :2633-2635