Epigenetics in the modern era of crop improvements

doi:10.1007/s11427-024-2784-3

Review

. 2025 Jun;68(6):1570-1609.

doi: 10.1007/s11427-024-2784-3. Epub 2025 Jan 8.

Epigenetics in the modern era of crop improvements

Yan Xue¹, Xiaofeng Cao², Xiangsong Chen³, Xian Deng⁴, Xing Wang Deng⁵, Yong Ding⁶, Aiwu Dong⁷, Cheng-Guo Duan⁸, Xiaofeng Fang⁹, Lei Gong¹⁰, Zhizhong Gong^{11

12}, Xiaofeng Gu¹³, Chongsheng He¹⁴, Hang He¹⁵, Shengbo He¹⁶, Xin-Jian He¹⁷, Yan He¹⁸, Yuehui He¹⁹, Guifang Jia²⁰, Danhua Jiang²¹, Jianjun Jiang²², Jinsheng Lai^{23

24

25

26

27}, Zhaobo Lang²⁸, Chenlong Li²⁹, Qing Li³⁰, Xingwang Li³¹, Bao Liu³², Bing Liu³³, Xiao Luo³⁴, Yijun Qi³⁵, Weiqiang Qian³⁶, Guodong Ren³⁷, Qingxin Song³⁸, Xianwei Song³⁹, Zhixi Tian⁴⁰, Jia-Wei Wang⁴¹, Yuan Wang⁴², Liang Wu⁴³, Zhe Wu⁴⁴, Rui Xia⁴⁵, Jun Xiao⁴⁶, Lin Xu⁴⁷, Zheng-Yi Xu⁴⁸, Wenhao Yan⁴⁹, Hongchun Yang⁵⁰, Jixian Zhai⁵¹, Yijing Zhang⁵², Yusheng Zhao⁵³, Xuehua Zhong⁵⁴, Dao-Xiu Zhou^{55

56}, Ming Zhou⁵⁷, Yue Zhou⁵⁸, Bo Zhu⁵⁹, Jian-Kang Zhu⁶⁰, Qikun Liu⁶¹

Affiliations

¹ State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. yan.xue@pku-iaas.edu.cn.
² State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xfcao@genetics.ac.cn.
³ State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. chen.xs@whu.edu.cn.
⁴ State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xdeng@genetics.ac.cn.
⁵ State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. deng@pku.edu.cn.
⁶ School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China. dingyong@ustc.edu.cn.
⁷ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. aiwudong@fudan.edu.cn.
⁸ Key Laboratory of Plant Design, National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. cgduan@cemps.ac.cn.
⁹ Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. xffang@tsinghua.edu.cn.
¹⁰ Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. gongl100@nenu.edu.cn.
¹¹ State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. gongzz@cau.edu.cn.
¹² College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China. gongzz@cau.edu.cn.
¹³ Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. guxiaofeng@caas.cn.
¹⁴ College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha, 410082, China. cshe@hnu.edu.cn.
¹⁵ Institute of Advanced Agricultural Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. hehang@pku.edu.cn.
¹⁶ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China. shengbo.he@scau.edu.cn.
¹⁷ National Institute of Biological Sciences, Beijing, 102206, China. hexinjian@nibs.ac.cn.
¹⁸ Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yh352@genetic.ac.cn.
¹⁹ School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yhhe@pku.edu.cn.
²⁰ Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. guifangjia@pku.edu.cn.
²¹ Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. dhjiang@genetics.ac.cn.
²² State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou, 450046, China. jjiang@henu.edu.cn.
²³ State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁴ Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁵ Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁶ Sanya Institute of China Agricultural University, Sanya, 572025, China. jlai@cau.edu.cn.
²⁷ Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China. jlai@cau.edu.cn.
²⁸ Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China. langzb@sustech.edu.cn.
²⁹ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. lichlong3@mail.sysu.edu.cn.
³⁰ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. qingli@mail.hzau.edu.cn.
³¹ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. xingwangli@mail.hzau.edu.cn.
³² Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. baoliu@nenu.edu.cn.
³³ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. bingliu@fudan.edu.cn.
³⁴ Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. xiao.luo@pku-iaas.edu.cn.
³⁵ Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. qiyijun@tsinghua.edu.cn.
³⁶ School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. wqqian@pku.edu.cn.
³⁷ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. gdren@fudan.edu.cn.
³⁸ State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China. qxsong@njau.edu.cn.
³⁹ Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xwsong@genetics.ac.cn.
⁴⁰ Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. zxtian@genetics.ac.cn.
⁴¹ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. jwwang@sippe.ac.cn.
⁴² Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yuan.wang@genetic.ac.cn.
⁴³ Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China. liangwu@zju.edu.cn.
⁴⁴ Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. wuz@sustech.edu.cn.
⁴⁵ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China. rxia@scau.edu.cn.
⁴⁶ Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. jxiao@genetics.ac.cn.
⁴⁷ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. xulin@cemps.ac.cn.
⁴⁸ Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. xuzy100@nenu.edu.cn.
⁴⁹ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. yanwenhao@mail.hzau.edu.cn.
⁵⁰ State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. h.yang@whu.edu.cn.
⁵¹ Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. zhaijx@sustech.edu.cn.
⁵² State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. Zhangyijing@fudan.edu.cn.
⁵³ Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yusheng.zhao@genetics.ac.cn.
⁵⁴ Department of Biology, Washington University in St. Louis, St. Louis, 63130, USA. xuehuazhong@wustl.edu.
⁵⁵ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. dao-xiu.zhou@universite-paris-saclay.fr.
⁵⁶ Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France. dao-xiu.zhou@universite-paris-saclay.fr.
⁵⁷ State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. mingzhou@zju.edu.cn.
⁵⁸ State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yue_zhou@pku.edu.cn.
⁵⁹ Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China. bozhu@sicnu.edu.cn.
⁶⁰ Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China. zhujk@sustech.edu.cn.
⁶¹ State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. qikunliu@pku.edu.cn.

PMID: 39808224
DOI: 10.1007/s11427-024-2784-3

Review

Epigenetics in the modern era of crop improvements

Yan Xue et al. Sci China Life Sci. 2025 Jun.

. 2025 Jun;68(6):1570-1609.

doi: 10.1007/s11427-024-2784-3. Epub 2025 Jan 8.

Authors

Affiliations

¹ State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. yan.xue@pku-iaas.edu.cn.
² State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xfcao@genetics.ac.cn.
³ State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. chen.xs@whu.edu.cn.
⁴ State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xdeng@genetics.ac.cn.
⁵ State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. deng@pku.edu.cn.
⁶ School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China. dingyong@ustc.edu.cn.
⁷ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. aiwudong@fudan.edu.cn.
⁸ Key Laboratory of Plant Design, National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. cgduan@cemps.ac.cn.
⁹ Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. xffang@tsinghua.edu.cn.
¹⁰ Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. gongl100@nenu.edu.cn.
¹¹ State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. gongzz@cau.edu.cn.
¹² College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China. gongzz@cau.edu.cn.
¹³ Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. guxiaofeng@caas.cn.
¹⁴ College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha, 410082, China. cshe@hnu.edu.cn.
¹⁵ Institute of Advanced Agricultural Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. hehang@pku.edu.cn.
¹⁶ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China. shengbo.he@scau.edu.cn.
¹⁷ National Institute of Biological Sciences, Beijing, 102206, China. hexinjian@nibs.ac.cn.
¹⁸ Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yh352@genetic.ac.cn.
¹⁹ School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yhhe@pku.edu.cn.
²⁰ Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. guifangjia@pku.edu.cn.
²¹ Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. dhjiang@genetics.ac.cn.
²² State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou, 450046, China. jjiang@henu.edu.cn.
²³ State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁴ Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁵ Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China. jlai@cau.edu.cn.
²⁶ Sanya Institute of China Agricultural University, Sanya, 572025, China. jlai@cau.edu.cn.
²⁷ Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China. jlai@cau.edu.cn.
²⁸ Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China. langzb@sustech.edu.cn.
²⁹ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. lichlong3@mail.sysu.edu.cn.
³⁰ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. qingli@mail.hzau.edu.cn.
³¹ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. xingwangli@mail.hzau.edu.cn.
³² Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. baoliu@nenu.edu.cn.
³³ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. bingliu@fudan.edu.cn.
³⁴ Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China. xiao.luo@pku-iaas.edu.cn.
³⁵ Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. qiyijun@tsinghua.edu.cn.
³⁶ School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. wqqian@pku.edu.cn.
³⁷ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. gdren@fudan.edu.cn.
³⁸ State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China. qxsong@njau.edu.cn.
³⁹ Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. xwsong@genetics.ac.cn.
⁴⁰ Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. zxtian@genetics.ac.cn.
⁴¹ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. jwwang@sippe.ac.cn.
⁴² Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yuan.wang@genetic.ac.cn.
⁴³ Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China. liangwu@zju.edu.cn.
⁴⁴ Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. wuz@sustech.edu.cn.
⁴⁵ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China. rxia@scau.edu.cn.
⁴⁶ Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. jxiao@genetics.ac.cn.
⁴⁷ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. xulin@cemps.ac.cn.
⁴⁸ Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China. xuzy100@nenu.edu.cn.
⁴⁹ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. yanwenhao@mail.hzau.edu.cn.
⁵⁰ State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. h.yang@whu.edu.cn.
⁵¹ Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. zhaijx@sustech.edu.cn.
⁵² State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. Zhangyijing@fudan.edu.cn.
⁵³ Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. yusheng.zhao@genetics.ac.cn.
⁵⁴ Department of Biology, Washington University in St. Louis, St. Louis, 63130, USA. xuehuazhong@wustl.edu.
⁵⁵ National Key Laboratory of Crop Genetic Improvement, Huebei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. dao-xiu.zhou@universite-paris-saclay.fr.
⁵⁶ Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France. dao-xiu.zhou@universite-paris-saclay.fr.
⁵⁷ State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. mingzhou@zju.edu.cn.
⁵⁸ State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yue_zhou@pku.edu.cn.
⁵⁹ Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China. bozhu@sicnu.edu.cn.
⁶⁰ Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China. zhujk@sustech.edu.cn.
⁶¹ State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China. qikunliu@pku.edu.cn.

PMID: 39808224
DOI: 10.1007/s11427-024-2784-3

Abstract

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

Keywords: crop improvement; epigenetics; plant development; plant immunity; stress responses.

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Conflict of interest statement

Compliance and ethics. The authors declare that they have no conflict of Interest.

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References

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1. Allis, C.D., and Jenuwein, T. (2016). The molecular hallmarks of epigenetic control. Nat Rev Genet 17, 487–500. - DOI
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[1] Allen, E., Xie, Z., Gustafson, A.M., and Carrington, J.C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207–221. - DOI

[2] Allen, E., Xie, Z., Gustafson, A.M., and Carrington, J.C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207–221. - DOI

[3] Allis, C.D., and Jenuwein, T. (2016). The molecular hallmarks of epigenetic control. Nat Rev Genet 17, 487–500. - DOI

[4] Allis, C.D., and Jenuwein, T. (2016). The molecular hallmarks of epigenetic control. Nat Rev Genet 17, 487–500. - DOI

[5] Alvarez-Venegas, R., Abdallat, A.A., Guo, M., Alfano, J.R., and Avramova, Z. (2007). Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2, 106–113. - DOI

[6] Alvarez-Venegas, R., Abdallat, A.A., Guo, M., Alfano, J.R., and Avramova, Z. (2007). Epigenetic control of a transcription factor at the cross section of two antagonistic pathways. Epigenetics 2, 106–113. - DOI

[7] Alvarez-Venegas, R., and Avramova, Z. (2002). SET-domain proteins of the Su(var)3-9, E(z) and Trithorax families. Gene 285, 25–37. - DOI

[8] Alvarez-Venegas, R., and Avramova, Z. (2002). SET-domain proteins of the Su(var)3-9, E(z) and Trithorax families. Gene 285, 25–37. - DOI

[9] Amara, U., Hu, J., Cai, J., and Kang, H. (2023). FLK is an mRNA m⁶A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis. Mol Plant 16, 919–929. - DOI

[10] Amara, U., Hu, J., Cai, J., and Kang, H. (2023). FLK is an mRNA m⁶A reader that regulates floral transition by modulating the stability and splicing of FLC in Arabidopsis. Mol Plant 16, 919–929. - DOI

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Epigenetics in the modern era of crop improvements

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Epigenetics in the modern era of crop improvements

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