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Epigenetics in the modern era of crop improvements

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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Melanin,DNA replication,and autophagy affect appressorium development in Setosphaeria turcica by regulating glycerol accumulation and metabolism

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Journal of Integrative Agriculture 2022年第3期21卷 762-773页

作者： GUO Xiao-yue LIU Ning LIU Bing-hui ZHOU Li-hong CAO Zhi-yan HAN Jian-min DONG Jin-gao State key laboratory of North China Crop Improvement and Regulation/key laboratory of hebei Province for plant physiology and molecular pathology/Mycotoxin and molecular plant pathology laboratory Hebei Agricultural UniversityBaoding 071001P.R.China

Setosphaeria turcica(*** turcicum)is the pathogenic fungus of maize(Zea mays)that causes northern leaf blight,which is a major maize disease *** appressoria are highly specialized infection structures formed by germinated conidia of *** that infect maize *** appressorium penetrates the plant cuticle by generating turgor,and glycerol is known to be the main source of the ***,the infection position penetrated by the appressorium on maize leaves was investigated,most of the germinated conidia entered the leaf interior by directly penetrating the epidermal cells,and the appressorium structure was necessary for the infection,whether it occurred through epidermal cells or ***,to investigate the effects of key factors in the development of the appressorium,we studied the effects of three inhibitors,including a melanin inhibitor(tricyclazole,TCZ),a DNA replication inhibitor(hydroxyurea,HU),and an autophagy inhibitor(3-methyladenine,3-MA),on appressorium turgor and glycerol *** results,appressorium turgor pressure and glycerol concentration in the appressorium reached their highest levels at the mature stage of the appressorium under the control and inhibitor *** three inhibitors had the greatest effects on appressorium turgor pressure at this *** and liposomes are the main substances producing *** was also found inhibitors affected the distribution of glycogen and liposomes,which were detected in the conidia,the germ tube,and the appressorium during appressorium *** study provides profound insight into the relationship between appressorium turgor pressure and glycerol content,which was affected by the synthesis of melanin,DNA replication,and autophagy in the developing appressorium during a *** infection.

关键词： melanin DNA replication autophagy appressorium development Setosphaeria turcica glycerol

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Genetic diversity and population structure of Commelina communis in China based on simple sequence repeat markers

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Journal of Integrative Agriculture 2018年第10期17卷 2292-2301页

作者： YANG Juan YU Hai-yan LI Xiang-ju DONG Jin-gao key laboratory of hebei Province for plant physiology and molecular pathology College of Life Science Hebei Agricultural University key laboratory of Weed and Rodent Biology and Management Institute of Plant Protection Chinese Academy of Agricultural Sciences

Commelina communis（Asiatic dayflower） is a troublesome weed in China. Genetic variation of 46 C. communis populations from different collection sites in our country was investigated using 12 simple sequence repeat（SSR） primer pairs. Polymorphism analysis results showed high level of genetic diversity among these populations. The alleles（bands） were amplified by these primer pairs. The polymorphic proportion was 18.25%, and the average polymorphism information content was 0.1330. The highest effective number of alleles was 1.9915 at locus YP33, and the lowest value was 1.0000 at both loci YP25 and YP31. C. communis showed major average observed heterozygosity value（0.8655） than that of average expected heterozygosity（0.1330）. C. communis populations were divided into three groups on the basis of unweighted pair-group method with arithmetic mean cluster analysis（Dice genetic similarity coefficient=0.772） and genetic structure analysis（K=3）, and a principal coordinate analysis. The results of this study further illustrated that C. communis populations contained abundant genetic information, and the 12 SSR markers could detect the microsatellite loci of C. communis genomic DNA. These results might indicate that C. communis maintains high genetic diversity among different populations.

关键词： Commelina communis UPGMA population structure principal component analysis microsatellite

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ZmMYC7 directly regulates ZmERF147 to increase maize resistance to Fusarium graminearum

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The Crop Journal 2023年第1期11卷 79-88页

作者： Hongzhe Cao Kang Zhang Wei Li Xi Pang Pengfei Liu Helong Si Jinping Zang Jihong Xing Jingao Dong State key laboratory of North China Crop Improvement and Regulation Hebei Agricultural UniversityBaoding 071000HebeiChina hebei key laboratory of plant physiology and molecular pathology Hebei Agricultural UniversityBaoding 071000HebeiChina

The jasmonic acid(JA)signaling pathway is involved in plant growth,development,and response to abiotic or biotic ***2,a bHLH transcription factor,is a regulatory hub in the *** function of ZmMYC7,a putative MYC2 ortholog,in jasmonate-signaled defense responses of maize has not been *** this study,we found that ZmMYC7 possesses JID,TAD,bHLH and Zip domains and essential characteristics of transcription factors:a nuclear location and transactivation *** ZmMYC7mutants showed markedly increased sensitivity to Fusarium graminearum and Setosphaeria *** expression levels of the defense-associated genes ZmPR1,ZmPR2,ZmPR3,ZmPR5,ZmPR6,and ZmPR7 in response to *** infection were downregulated in ZmMYC7 mutants,while ZmPR4 and ZmPR10 were ***7 interacted with members of the ZmJAZ family,including ZmJAZ8,ZmJAZ11,and ***7 physically interacted with G-box cis-elements in the ZmERF147 promoter in vitro and transcriptional activation of ZmERF147 by ZmMYC7 was inhibited by ZmJAZ11 and ***147 mutants were more susceptible to *** infection than inbred line B73with concomitant down-regulation of all defense-associated ZmPRs except *** findings indicate that ZmMYC7 functions in maize resistance to *** and sheds light on maize defense responses to pathogenic fungi via the JA signaling pathway.

关键词： Maize Fusarium graminearum ZmMYC7 ZmERF147

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BcSDR1 is involved in regulation of glucose transport and cAMP and MAPK signaling pathways in Botrytis cinerea

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Journal of Integrative Agriculture 2022年第9期21卷 2628-2640页

作者： SI He-long ZHANG Kang LI Bai YUAN Xue-mei ZANG Jin-ping CAO Hong-zhe XING Ji-hong DONG Jin-gao State key laboratory of North China Crop Improvement and Regulation Hebei Agricultural UniversityBaoding 071000P.R.China hebei key laboratory of plant physiology and molecular pathology Hebei Agricultural UniversityBaoding 071000P.R.China

Botrytis cinerea is a typical necrotrophic pathogenic fungus that causes severe diseases in a wide range of plant species, leading to significant economic losses. Our previous study showed that BcSDR1 positively regulates growth,development, and pathogenicity of B. cinerea. However, the regulation mechanism of BcSDR1 and the relationship between BcSDR1 and cAMP and MAPK signaling pathways are not well understood. In this study, transcriptome data showed that BcSDR1 is involved in glucose transmembrane transport, signal transduction, secondary metabolism, and other biological processes. BcSDR1 mutant(BCt41) showed remarkably weak sensitivity to cAMP and MAPK signaling pathways specific inhibitors, SQ22536 and U0126, and significantly decreased cAMP content. The key genes of cAMP and MAPK signaling pathways, BcGB1, BcBTP1, BcBOS1, BcRAS1, and BcBMP3 were significantly upregulated,whereas BcPLC1, BcBCG1, BcCDC4, BcSAK1, BcATF1, and BcBAP1 were significantly downregulated(P<0.05).BcSDR1 was obviously upregulated in BcBCG2, BcBCG3, BcPKA1, and BcPKAR RNA interference(RNAi) mutants, but significantly downregulated in BcPKA2, BcBMP1, and BcBMP3 RNAi mutants. Thus, BcBCG2, BcBCG3, BcPKA1, and BcPKAR negatively regulate BcSDR1 expression, whereas BcPKA2, BcBMP1, and BcBMP3 positively regulate BcSDR1expression.

关键词： Botrytis cinerea BcSDR1 glucose transmembrane transport cAMP signaling pathway MAPK signaling pathway

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GST family genes in jujube actively respond to phytoplasma infection

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Horticultural plant Journal 2024年第1期10卷 77-90页

作者： Qipeng Wang Liman Zhang Chaoling Xue Yao Zhang Xiangrui Meng Zhiguo Liu Mengjun Liu Jin Zhao College of Life Science Hebei Agricultural UniversityBaodingHebei 071000China hebei key laboratory of plant physiology and molecular pathology Hebei Agricultural UniversityBaodingHebei 071000China Research Center of Chinese Jujube Hebei Agricultural UniversityBaodingHebei 071000China

Jujube witches’broom(JWB)caused by phytoplasma has a severely negative effect on multiple metabolisms in *** GST gene family in plants participates in the regulation of a variety of biotic and abiotic *** study aims to identify and reveal the changes in the jujube GST gene family in response to phytoplasma ***,70 ZjGSTs were identified in the jujube genome and divided into 8 *** them,the Tau-class,including 44 genes,was the *** analysis indicated that Tau-class genes were highly conserved among species,such as Arabidopsis,cotton,chickpea,and *** chromosome location analysis,37.1%of genes were clustered,and 8 of 9 gene clusters were composed of Tau class *** RT-PCR,qRT-PCR and enzyme activity detection,the results showed that the expression of half(20/40)of the tested ZjGSTs was inhibited by phytoplasma infection in field and tissue culture conditions,and GST activity was also significantly *** the resistant and susceptible varieties under phytoplasma infection,ZjGSTU49-ZjGSTU54 in the cluster IV showed opposite expression patterns,which may be due to functional divergence during *** upregulated genes(ZjGSTU45,ZjGSTU49,ZjGSTU59,and ZjGSTU70)might be involved in the process of jujube against *** yeast two-hybrid results showed that all 6 Tauclass proteins tested could form homodimers or ***,the comprehensive analysis of the jujube GST gene family revealed that ZjGSTs responded actively to phytoplasma ***,some screened genes(ZjGSTU24,ZjGSTU49-52,ZjGSTU70,and ZjDHAR10)will contribute to further functional studies of jujube-phytoplasma interactions.

关键词： Chinese jujube GST gene Family Phytoplasma Gene cluster Expression Protein interaction

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Bioinformatic analysis and functional characterization of CFEM proteins in Setosphaeria turcica

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Journal of Integrative Agriculture 2021年第9期20卷 2438-2449页

作者： WANG Jian-xia LONG Feng ZHU Hang ZHANG Yan WU Jian-ying SHEN Shen DONG Jin-gao HAO Zhi-min State key laboratory of North China Crop Improvement and Regulation/key laboratory of hebei Province for plant physiology and molecular pathology College of Life SciencesHebei Agricultural UniversityBaoding 071001P.R.China College of plant Protection Hebei Agricultural UniversityBaoding 071001P.R.China

Common in Fungal Extracellular Membrane(CFEM)domains are uniquely found in fungal extracellular membrane proteins which are important for *** study identified 13 StCFEM proteins in the genome of Setosphaeria turcica,the hemibiotrophic fungus that causes northern corn leaf *** alignment and WebLogo analysis of their CFEM domains indicated that the amino acids were highly conserved and that,with the exception of StCFEM1,2,3,and 6,they contained eight *** analysis suggested that these 13 proteins(StCFEM1–13)could be divided into 2 clades based on the presence of the trans-membrane *** StCFEM proteins with a signal peptide and without a trans-membrane domain were considered as candidate effector *** CFEM domain in the candidate effector proteins could form a helical-basket structure homologous to Csa2 in Candida *** analysis suggested that the 13 genes were expressed during fungal infection and a yeast secretion assay revealed that these candidate effectors were secreted *** was also found that StCFEM3,4,and 5 couldn't affect BAX/INF1-induced programmed cell death(PCD)in Nicotiana benthamiana and while StCFEM12 could suppress INF1-induced PCD,it showed no effect on BAXinduced *** study found that there were 13 members of the *** CFEM protein family and that StCFEM12 was a candidate *** study laid the foundation for illustrating the roles of CFEM proteins during the pathogenic processes of phytopathogens.

关键词： CFEM domain effector Setosphaeria turcica signal peptide PCD

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A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell

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Journal of Integrative plant Biology 2014年第6期56卷 539-549页

作者： Kezhen Yangy Min Jiangy Jie Le key laboratory of plant molecular physiology Institute of Botany the Chinese Academy of Sciences

In Arabidopsis thaliana L., stomata are produced through a series of divisions including asymmetric and symmetric divisions. Asymmetric entry division of meristemoid mother cellproduces two daughter cells, the smal er meristemoid and the larger sister cell, a stomatal lineage ground cell（SLGC）. Stomatal lineage ground cells can differentiate into epidermal pavement cells but have the potential to divide asymmetrical y, spacing divisions, to create satel ite meristemoids. Peptide ligands and TOO MANY MOUTHS （TMM） and ERECTA family receptors regulate the initiation of stomatal lineages, activity, and orientation of spacing divisions. Here, we reported that a natural mutant 28y displayed an increased stomatal density and index. Using map-based cloning, we identified mutation in ARGONAUTE1 （AGO1） as the cause of 28y phenotypes. Time-lapse tracing of stomatal lineage cells reveals that stomatal overproduction in 28y is caused by the excessive asymmetric spacing division of *** genetic results demonstrated that AGO1 acts down-stream of TMM and negatively regulates the SPCH transcripts, but in a brassinosteroid-independent manner. Upregulation of AGAMOUS-LIKE16 （AGL16） in 28y mutants suggests that AGO1 is required to restrict AGL16-mediated stomatal spacing divisions, an miRNA pathway in addition to ligand-receptor signaling modules.

关键词： Arabidopsis ARGONAUTEI cell division stomatal development

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plant villins: Versatile actin regulatory proteins

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Journal of Integrative plant Biology 2015年第1期57卷 40-49页

作者： Shanjin Huang Xiaolu Qu Ruihui Zhang key laboratory of plant molecular physiology Institute of Botany the Chinese Academy of Sciences

Regulation of actin dynamics is a central theme in cell biology that is important for different aspects of cell physiology. Villin, a member of the villin/gelsolin/fragmin superfamily of proteins, is an important regulator of actin. Villins contain six gelsolin homology domains （G1-G6） and an extra headpiece domain. In contrast to their mammalian counterparts, plant villins are expressed widely, implying that plant villins play a more general role in regulating actin dynamics. Some plant villins have a defined role in modifying actin dynamics in the pollentube; most of their in vivo activities remain to be ascertained. Recently, our understanding of the functions and mechanisms of action for plant villins has progressed rapidly, primarily due to the advent of Arabidopsis thaliana genetic approaches and imaging capabilities that can visualize actin dynamics at the single filament level in vitro and in living plant cells. In this review, we focus on discussing the biochemical activities and modes of regulation of plant villins. Here, we present current understand- ing of the functions of plant villins. Finally, we highlight some of the key unanswered questions regarding the functions and regulation of plant villins for future research.

关键词： Actin bundle actin capping actin cytoskeleton filamentsevering villin

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Rice bZIP protein,REB,interacts with GCN4 motif in promoter of Waxy gene

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Science China(Life Sciences) 2002年第4期45卷 352-360页

作者：程世军洪孟民王宗阳 Shanghai Institute of plant physiology and National key laboratory of plant molecular Genetics Chinese Academy of Sciences Shanghai China

A bifactorial endosperm box (EB), which contains an endosperm motif (EM) and a GCN4 motif, was found in rice Wx promoter. EB was found in 5′ upstream region of many seed storage protein genes accounting for these genes expression exclusive in endosperm among various cereals. Many reports demonstrated that the bZIP transcription activators isolated from wheat, barley and maize, etc. regulate the gene expression through binding to the GCN4 motif. In this research, we showed that GCN4 sequence could be recognized by nuclear proteins extracted from immature rice seeds. Furthermore, a rice bZIP protein, REB was isolated by using PCR method and REB fusion protein was expressed in E. coli. The results of gel shift analysis showed that REB could recognize and bind to the GCN4 motif in the Wx gene in addition to binding to the target sequence in the promoter of α-globulin.

关键词： Wx gene, GCN4motif, REB.

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