IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31844-w.html
   My bibliography  Save this article

Natural variation of DROT1 confers drought adaptation in upland rice

Author

Listed:
  • Xingming Sun

    (China Agricultural University
    China Agricultural University)

  • Haiyan Xiong

    (China Agricultural University
    Huazhong Agricultural University)

  • Conghui Jiang

    (China Agricultural University)

  • Dongmei Zhang

    (Chinese Academy of Sciences)

  • Zengling Yang

    (China Agricultural University)

  • Yuanping Huang

    (China Agricultural University)

  • Wanbin Zhu

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Shuaishuai Ma

    (China Agricultural University)

  • Junzhi Duan

    (China Agricultural University)

  • Xin Wang

    (China Agricultural University)

  • Wei Liu

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Haifeng Guo

    (China Agricultural University)

  • Gangling Li

    (China Agricultural University)

  • Jiawei Qi

    (China Agricultural University)

  • Chaobo Liang

    (China Agricultural University)

  • Zhanying Zhang

    (China Agricultural University)

  • Jinjie Li

    (China Agricultural University)

  • Hongliang Zhang

    (China Agricultural University)

  • Lujia Han

    (China Agricultural University)

  • Yihua Zhou

    (Chinese Academy of Sciences)

  • Youliang Peng

    (China Agricultural University)

  • Zichao Li

    (China Agricultural University
    Sanya Institute of China Agricultural University)

Abstract

Upland rice is a distinct ecotype that grows in aerobic environments and tolerates drought stress. However, the genetic basis of its drought resistance is unclear. Here, using an integrative approach combining a genome-wide association study with analyses of introgression lines and transcriptomic profiles, we identify a gene, DROUGHT1 (DROT1), encoding a COBRA-like protein that confers drought resistance in rice. DROT1 is specifically expressed in vascular bundles and is directly repressed by ERF3 and activated by ERF71, both drought-responsive transcription factors. DROT1 improves drought resistance by adjusting cell wall structure by increasing cellulose content and maintaining cellulose crystallinity. A C-to-T single-nucleotide variation in the promoter increases DROT1 expression and drought resistance in upland rice. The potential elite haplotype of DROT1 in upland rice could originate in wild rice (O. rufipogon) and may be beneficial for breeding upland rice varieties.

Suggested Citation

  • Xingming Sun & Haiyan Xiong & Conghui Jiang & Dongmei Zhang & Zengling Yang & Yuanping Huang & Wanbin Zhu & Shuaishuai Ma & Junzhi Duan & Xin Wang & Wei Liu & Haifeng Guo & Gangling Li & Jiawei Qi & C, 2022. "Natural variation of DROT1 confers drought adaptation in upland rice," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31844-w
    DOI: 10.1038/s41467-022-31844-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31844-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-31844-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Dan Ye & Sintu Rongpipi & Sarah N. Kiemle & William J. Barnes & Arielle M. Chaves & Chenhui Zhu & Victoria A. Norman & Alexander Liebman-Peláez & Alexander Hexemer & Michael F. Toney & Alison W. Rober, 2020. "Preferred crystallographic orientation of cellulose in plant primary cell walls," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Wensheng Wang & Ramil Mauleon & Zhiqiang Hu & Dmytro Chebotarov & Shuaishuai Tai & Zhichao Wu & Min Li & Tianqing Zheng & Roven Rommel Fuentes & Fan Zhang & Locedie Mansueto & Dario Copetti & Millicen, 2018. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice," Nature, Nature, vol. 557(7703), pages 43-49, May.
    3. Simon C. Groen & Irina Ćalić & Zoé Joly-Lopez & Adrian E. Platts & Jae Young Choi & Mignon Natividad & Katherine Dorph & William M. Mauck & Bernadette Bracken & Carlo Leo U. Cabral & Arvind Kumar & Ro, 2020. "The strength and pattern of natural selection on gene expression in rice," Nature, Nature, vol. 578(7796), pages 572-576, February.
    4. Xuehui Huang & Nori Kurata & Xinghua Wei & Zi-Xuan Wang & Ahong Wang & Qiang Zhao & Yan Zhao & Kunyan Liu & Hengyun Lu & Wenjun Li & Yunli Guo & Yiqi Lu & Congcong Zhou & Danlin Fan & Qijun Weng & Chu, 2012. "A map of rice genome variation reveals the origin of cultivated rice," Nature, Nature, vol. 490(7421), pages 497-501, October.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Rujia Chen & Ning Xiao & Yue Lu & Tianyun Tao & Qianfeng Huang & Shuting Wang & Zhichao Wang & Mingli Chuan & Qing Bu & Zhou Lu & Hanyao Wang & Yanze Su & Yi Ji & Jianheng Ding & Ahmed Gharib & Huixin, 2023. "A de novo evolved gene contributes to rice grain shape difference between indica and japonica," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Daiqi Wang & Hongru Wang & Xiaomei Xu & Man Wang & Yahuan Wang & Hong Chen & Fei Ping & Huanhuan Zhong & Zhengkun Mu & Wantong Xie & Xiangyu Li & Jingbin Feng & Milan Zhang & Zhilan Fan & Tifeng Yang , 2023. "Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Changxuan Xia & Guohua Liang & Kang Chong & Yunyuan Xu, 2023. "The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Seung Young Lee & Hyun-Sook Lee & Chang-Min Lee & Su-Kyung Ha & Hyang-Mi Park & So-Myeong Lee & Youngho Kwon & Ji-Ung Jeung & Youngjun Mo, 2023. "Multi-Environment Trials and Stability Analysis for Yield-Related Traits of Commercial Rice Cultivars," Agriculture, MDPI, vol. 13(2), pages 1-13, January.
    5. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Ran Zhang & Zhen Hu & Yanting Wang & Huizhen Hu & Fengcheng Li & Mi Li & Arthur Ragauskas & Tao Xia & Heyou Han & Jingfeng Tang & Haizhong Yu & Bingqian Xu & Liangcai Peng, 2023. "Single-molecular insights into the breakpoint of cellulose nanofibers assembly during saccharification," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Chew, Soo Hong & Ebstein, Richard P. & Lu, Yunfeng, 2023. "Rice culture and the cushion hypothesis: Experimental evidence from incentivized risk taking tasks," Economics Letters, Elsevier, vol. 223(C).
    8. Hideki Yoshida & Ko Hirano & Kenji Yano & Fanmiao Wang & Masaki Mori & Mayuko Kawamura & Eriko Koketsu & Masako Hattori & Reynante Lacsamana Ordonio & Peng Huang & Eiji Yamamoto & Makoto Matsuoka, 2022. "Genome-wide association study identifies a gene responsible for temperature-dependent rice germination," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    10. Zihao Wang & Wenxi Wang & Xiaoming Xie & Yongfa Wang & Zhengzhao Yang & Huiru Peng & Mingming Xin & Yingyin Yao & Zhaorong Hu & Jie Liu & Zhenqi Su & Chaojie Xie & Baoyun Li & Zhongfu Ni & Qixin Sun &, 2022. "Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Elisa Zampieri & Michele Pesenti & Fabio Francesco Nocito & Gian Attilio Sacchi & Giampiero Valè, 2023. "Rice Responses to Water Limiting Conditions: Improving Stress Management by Exploiting Genetics and Physiological Processes," Agriculture, MDPI, vol. 13(2), pages 1-23, February.
    12. Yingyan Yu & Zhen Zhang & Xiaorui Dong & Ruixin Yang & Zhongqu Duan & Zhen Xiang & Jun Li & Guichao Li & Fazhe Yan & Hongzhang Xue & Du Jiao & Jinyuan Lu & Huimin Lu & Wenmin Zhang & Yangzhen Wei & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    13. Yajun Gou & Yueqin Heng & Wenyan Ding & Canhong Xu & Qiushuang Tan & Yajing Li & Yudong Fang & Xiaoqing Li & Degui Zhou & Xinyu Zhu & Mingyue Zhang & Rongjian Ye & Haiyang Wang & Rongxin Shen, 2024. "Natural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    14. Bin Yang & Jiali Zeng & Shaona Chen & Shengyu Li & Longmei Wu & Xiaorong Wan, 2022. "Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice," Agriculture, MDPI, vol. 13(1), pages 1-14, December.
    15. Decha Songtoasesakul & Wanchana Aesomnuk & Sarinthip Pannak & Jonaliza Lanceras Siangliw & Meechai Siangliw & Theerayut Toojinda & Samart Wanchana & Siwaret Arikit, 2023. "QTL-seq Identifies Pokkali-Derived QTLs and Candidate Genes for Salt Tolerance at Seedling Stage in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 13(8), pages 1-15, August.
    16. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    17. Chuanzhong Zhang & Hongru Wang & Xiaojie Tian & Xinyan Lin & Yunfei Han & Zhongmin Han & Hanjing Sha & Jia Liu & Jianfeng Liu & Jian Zhang & Qingyun Bu & Jun Fang, 2024. "A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    18. Xiaojuan Fan & Yongtao Cui & Jian Song & Honghuan Fan & Liqun Tang & Jianjun Wang, 2024. "Preliminary Exploration of Physiology and Genetic Basis Underlying High Yield in Indica–Japonica Hybrid Rice," Agriculture, MDPI, vol. 14(4), pages 1-12, April.
    19. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    20. Jingfen Huang & Yilin Zhang & Yapeng Li & Meng Xing & Cailin Lei & Shizhuang Wang & Yamin Nie & Yanyan Wang & Mingchao Zhao & Zhenyun Han & Xianjun Sun & Han Zhou & Yan Wang & Xiaoming Zheng & Xiaoron, 2024. "Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31844-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.