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Epigenetics in the modern era of crop improvements

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Science China Life Sciences 2025年

作者： Yan Xue Xiaofeng Cao Xiangsong Chen Xian Deng Xingwang Deng Yong Ding Aiwu Dong Chengguo Duan Xiaofeng Fang Lei Gong Zhizhong Gong Xiaofeng Gu Chongsheng He Hang He Shengbo He Xinjian He Yan He Yuehui He Guifang Jia Danhua Jiang Jianjun Jiang Jinsheng Lai Zhaobo Lang Chenlong Li Qing Li Xingwang Li Bao Liu Bing Liu Xiao Luo Yijun Qi Weiqiang Qian Guodong Ren Qingxin Song Xianwei Song Zhixi Tian Jiawei Wang Yuan Wang Liang Wu Zhe Wu Rui Xia Jun Xiao Lin Xu Zhengyi Xu Wenhao Yan Hongchun Yang Jixian Zhai Yijing Zhang Yusheng Zhao Xuehua Zhong Daoxiu Zhou Ming Zhou Yue Zhou Bo Zhu Jiankang Zhu Qikun Liu College of Life Sciences Institute of Life Science and Green Development Hebei University biotechnology Research Institute Chinese Academy of Agricultural Sciences College of biology Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan Engineering and Technology Research Center of Hybrid Rapeseed Hunan University Institute of Advanced Agricultural Sciences School of Advanced Agricultural Sciences Peking University State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University National Institute of Biological Sciences Key Laboratory of Seed Innovation Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Advanced Agricultural Sciences Peking-Tsinghua Center for Life Sciences Peking University 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 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 State Key Laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in Weifang State Key Laboratory of Crop Stress Adaptation and Improvement School of Life Sciences Henan University State Key Laboratory of Maize Bio-breeding National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University Frontiers Science Center for molecular Design Breeding China Agricultural University Center for Crop Functional Genomics and molecular Breeding China Agricultural University Sanya Institute of China Agricultural University Hainan Yazhou Bay Seed Laboratory Institute of Advan

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.

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Optimisation of Adventitious Shoot Regeneration and Agrobacterium-mediated Transformation in Canna × generalis(Canna Lily)

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Horticultural Plant Journal 2019年第1期5卷 39-46页

作者： Rani Singh Arvind Kumar Dubey Indraneel Sanyal Plant Transgenic Laboratory Division of Molecular Biology and Biotechnology CSIR-National Botanical Research Institute

Canna being ornamental plants has a significant role in agriculture, medical, economy and food industry. Canna has a limited vase life due to the rapid loss of moisture from its perianth. For improving its market value, cuticularisation of the perianth can be achieved by the expression of a heterologous cutin producing gene, using the tissue culture and transformation protocol developed in this study. Efficient, rapid and direct adventitious shoot regeneration was successfully established in Canna × generalis using recalcitrant rhizome explants. The explants were cultured on MS medium supplemented with 6-benzylaminopurine(6-BA), thidiazuron(TDZ), and kinetin. Among the four genotypes taken for tissue culture, the ‘Trinacria variegata' was the best responding cultivar. And 2 mg · L^(-1)6-BA or 1.5 mg · L^(-1) TDZ along with 0.1 mg · L^(-1) IAA was optimum for their regeneration. The highest regeneration was achieved in ‘Trinacria variegata'(36%) on 6-BA, 33% on TDZ while kinetin failed to evoke any regenerative responses. Regeneration was enhanced by supplementation of 100 mg · L^(-1) ascorbic acid(AsA), while, 100 mg · L^(-1) of l-cysteine or 100 mg · L^(-1) dithiothreitol(DTT), inhibited regeneration. Shoots were observed to develop 3–5 fibrous roots on MS medium supplemented with 0.5 mg · L^(-1) indole-3-butyric acid(IBA). The plantlets were transplanted into pots and acclimatised in glasshouse with 100%survival. For transformation of Canna, rhizome explants were co-cultivated for 60 min in Agrobacterium suspension. The explants were washed with 500 mg · L^(-1) cefotaxime solution, subjected to 100 mg · L^(-1) kanamycin selection followed by excision of the shoots and culturing them on IBA-supplemented media for root development. Transgene integration in the putative transformants was confirmed by PCR assay and copy number by Southern blot hybridisation analysis.

关键词： Canna regeneration rhizome UidA Agrobacterium transformation ascorbic acid 6-BA TDZ

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World Journal of Gastroenterology 2016年第30期22卷 6800-6816页

作者： Mahmoud Fathy Dondeti Eman Anwar El-Maadawy Roba Mohamed Talaat Genetic Engineering and biotechnology Research division National Research Centre molecular biology Department Genetic Engineering and Biotechnology Research Institute University of Sadat City

Hepatocellular carcinoma(HCC) is a primary liver cancer, which is one of the most prevalent cancers among humans. Many factors are involved in the liver carcinogenesis as lifestyle and environmental factors. Hepatitis virus infections are now recognized as the chief etiology of HCC; however, the precise mechanism is still enigmatic till now. The inflammation triggered by the cytokine-mediated immune response, was reported to be the closest factor of HCC development. Cytokines are immunoregulatory proteins produced by immune cells, functioning as orchestrators of the immune response. Genes of cytokines and their receptors are known to be polymorphic, which give rise to variations in their genes. These variations have a great impact on the expression levels of the secreted cytokines. Therefore, cytokine gene polymorphisms are involved in the molecular mechanisms of several diseases. This piece of work aims to shed much light on the role of cytokine gene polymorphisms as genetic host factor in hepatitis related HCC.

关键词： Hepatocellular carcinoma Hepatitis C virus Hepatitis B virus Cytokines Polymorphism

Evaluating the effectiveness of marine actinobacterial extract and its mediated titanium dioxide nanoparticles in the degradation of azo dyes

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Journal of Environmental Sciences 2014年第4期26卷 775-782页

作者： S Priyaragini S Veena D Swetha L Karthik G Kumar K V Bhaskara Rao molecular and Microbiology Research Laboratory Environmental Biotechnology Division School of Bio Sciences and Technology VIT University

Aim of the present study was to synthesize titanium dioxide nanoparticles （YiO2 NPs） from marine actinobacteria and to develop an eco-friendly azo-dye degradation method. A total of five actinobacterial isolates were isolated from Chennai marine sediments, Tamilnadu, India and analyzed for the synthesis of TiO2 NPs using titanium hydroxide. Among these, the isolate PSV 3 showed positive results for the synthesis of TiO2 NPs, which was confirmed by UV analysis. Further characterization of the synthesized TiO2 NPs was done using XRD, AFM and FI＇-IR analysis. Actinobacterial crude extract and synthesized TiO2 NPs was found efficient in degrading azo dye such as Acid Red 79 （AR-79） and Acid Red 80 （AR-80）. Degradation percentage was found to be 81% for AR-79, 83% for AR-80 using actinobacterial crude extract and 84% for AR-79, 85% for AR-80 using TiO2 NPs. Immobilized actinobacterial ceils showed 88% for AR-79 and 81% for AR- 80, dye degrading capacity. Degraded components were characterized by FT-IR and GC-MS analysis. The phytotoxicity test with 500 μg/mL of untreated dye showed remarkable phenotypic as well as cellular damage to Tagetes erecta plant. Comparatively no such damage was observed on plants by degraded dye components. In biotoxicity assay, treated dyes showed less toxic effect as compared to the untreated dyes.

关键词： actinobacteria azo dye degradation ZiO2 NPs biotoxicity Tagetes erecta

A Myosin XI Tail Domain Homologous to the Yeast Myosin Vacuole-Binding Domain Interacts with Plastids and Stromules in Nicotiana benthamiana

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molecular Plant 2009年第6期2卷 1351-1358页

作者： Amir Sattarzadeh Johanna Krahmer Arnaud D. Germain Maureen R. Hanson Department of molecular biology and Genetics Biotechnology Building Cornell University Ithaca NY 14853 USA

The actin cytoskeleton plays a role in mobility of many different organelles in plant cells, including chloroplasts, mitochondria, Golgi, and peroxisomes. While progress has been made in identifying the myosin motors involved in trafficking of various plant organelles, not all of the cargoes mobilized by different members of the myosin XI family have yet been identified. The involvement of myosins in chloroplast positioning and mitochondrial movement was demonstrated by expression of a virus-induced gene silencing （VIGS） construct in tobacco. When VIGS with two different conserved sequences from a myosin Xl motor was performed in plants with either GFP-labeled plastids or mitochondria, chloroplast positioning in the dark was abnormal, and mitochondrial movement ceased. Because these and prior obser- vations have implicated a role for myosins and the actin cytoskeleton in plastid and stromule movement, we searched for myosin tail domains that could associate with plastids and stromules. While a yellow fluorescent protein （YFP） fusion with the entire tail region of myosin XI-F was usually found only in the cytoplasm, we observed that an Arabidopsis or Nicotiana benthamiana YFP：：myosin XI-F tail domain homologous to the yeast myo2p vacuole-binding domain associated with plastids and stromules after transient expression in N. benthamiana. Taken together, these observations implicate myosin motor proteins in dynamics of plastids and stromules.

关键词： Chloroplast biology cytoskeleton dynamics mitochondria gene silencing fluorescent protein.

Calcium and Calmodulin-Mediated Regulation of Gene Expression in Plants

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molecular Plant 2009年第1期2卷 13-21页

作者： Min Chul Kim Woo Sik Chung Dae-Jin Yun Moo Je Cho division of Applied Life Science (BK21 Program) Plant Molecular Biology and Biotechnology Research Center and Environmental Biotechnology National Core Research Center Gyeongsang National University Jinju 660-701 Korea

Sessile plants have developed a very delicate system to sense diverse kinds of endogenous developmental cues and exogenous environmental stimuli by using a simple Ca^2＋ ion. Calmodulin （CAM） is the predominant Ca^2＋ sensor and plays a crucial role in decoding the Ca^2＋ signatures into proper cellular responses in various cellular compartments in eukaryotes. A growing body of evidence points to the importance of Ca^2＋ and CaM in the regulation of the transcriptional process during plant responses to endogenous and exogenous stimuli. Here, we review recent progress in the identification of transcriptional regulators modulated by Ca^2＋ and CaM and in the assessment of their functional significance during plant signal transduction in response to biotic and abiotic stresses and developmental cues.

关键词： Abiotic/environmental stress calcium signaling/transport gene expression.

Doxycycline blocks gastric ulcer by regulating matrix metalloproteinase-2 activity and oxidative stress

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World Journal of Gastroenterology 2011年第28期17卷 3310-3321页

作者： Laishram Pradeepkumar Singh Amartya Mishra Debjit Saha Snehasikta Swarnakar Department of Physiology Drug Development Diagnostics and Biotechnology DivisionIndian Institute of Chemical Biology

AIM: To examine the effect of doxycycline on the activity of matrix metalloproteinases (MMPs) and oxidative stress in gastric tissues of rats following gastric ***: Gastric ulcers were generated in rats by administration of 70% ethanol,and activity of doxycycline was tested by administration 30 min prior to ***,the effect of doxycycline was tested in an indomethacin-induced gastric ulcer *** activities and expression of MMPs were examined by zymography and Western blot ***: Gastric injury in rats as judged by elevated ulcer indices following exposure to ulcerogen,either indomethacin or ethanol,was reversed significantly by ***-induced ulcerated gastric tissues exhibited about 12-fold higher proMMP-9 activity and about 5-fold higher proMMP-3 activity as compared to control ***,ethanol induced about 22-fold and about 6-fold higher proMMP-9 and proMMP-3 activities,respectively,in rat gastric *** proMMP-9 and MMP-3 activities were markedly decreased by doxycycline in ulcerogen treated rat gastric *** contrast,the reduced MMP-2 activity in ulcerated tissues was increased by doxycycline during ulcer *** the other hand,doxycycline inhibited significantly proMMP-9,-2 and -3 activities in *** addition,doxycycline reduced oxidative load in gastric tissues and scavenged H2O2 in *** results suggest a novel regulatory role of doxycycline on MMP-2 activity in addition to inhibitory action on MMP-9 and MMP-3 during prevention of gastric ***: This is the first demonstration of dual action of doxycycline,that is,regulation of MMP activity and reduction of oxidative stress in arresting gastric injury.

关键词： Doxycycline Extracellular matrix Matrix metalloproteinases Reactive oxygen species Tissue inhibitor of metalloproteinase

Biosynthesis of Callose and Cellulose by Detergent Extracts of Tobacco Cell Membranes and Quantification of the Polymers Synthesized in vitro

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Journal of Integrative Plant biology 2010年第2期52卷 221-233页

作者： Carolina Cifuentes Vincent Bulone Anne Mie C.Emons Laboratory of Plant Cell biology Wageningen University division of Glycoscience School of BiotechnologyRoyal Institute of TechnologyAlbaNova University Center Department of Biomolecular Systems FOM Institute for Atomic and Molecular Physics

The conditions that favor the in vitro synthesis of cellulose from tobacco BY-2 cell extracts were determined. The procedure leading to the highest yield of cellulose consisted of incubating digitonin extracts of membranes from 11-day-old tobacco BY-2 cells in the presence of 1 mM UDP-glucose, 8 mM Ca^2＋ and 8 mM Mg^2＋. Under these conditions, up to nearly 40% of the polysaccharides synthesized in vitro corresponded to cellulose, the other polymer synthesized being callose. Transmission electron microscopy analysis revealed the occurrence of two types of structures in the synthetic reactions. The first type consisted of small aggregates with a diameter between 3 and 5 nm that associated to form fibrillar strings of a maximum length of 400 nm. These structures were sensitive to the acetic/nitric acid treatment of Updegraff and corresponded to callose. The second type of structures was resistant to the Updegraff reagent and corresponded to straight cellulose microfibrils of 2-3 nm in diameter and 200 nm to up to 5 μm in length. In vitro reactions performed on electron microscopy grids indicated that the minimal rate of microfibril elongation in vitro is 120 nm/min. Measurements of retardance by liquid crystal polarization microscopy as a function of time showed that small groups of microfibrils increased in retardance by up to 0.047 nm/min per pixel, confirming the formation of organized structures.

关键词： Biosynthesis of Callose and Cellulose by Detergent Extracts of Tobacco Cell Membranes and Quantification of the Polymers Synthesized in vitro

Drought Stress Impairs Grain Yield and Quality of Rice Genotypes by Impaired Photosynthetic Attributes and K Nutrition

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Rice science 2020年第1期27卷 5-9页

作者： Muhammad Zahid MUMTAZ Muhammad SAQIB Ghulam ABBAS Javaid AKHTAR Zia Ul-QAMAR Institute of Soil and Environmental Sciences University of Agriculture Institute of molecular biology and biotechnology The University of Lahore Department of Environmental Sciences COMSATS University Plant Breeding and Genetics division Nuclear Institute for Agriculture and Biology

Drought is one of the most prevalent abiotic stresses that adversely affect rice productivity(Petrozza et al, 2014). Rice is very sensitive to drought stress and drought can cause 50% reduction in rice production globally(Yang et al, 2008). To meet the food needs for global population, 63% more agricultural production will be required by the year 2050 than.

关键词： drought Yield globally