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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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Gene Amplification and High-Level Expression of Human Pro-Urokinase cDNA in Chinese Hamster Ovary Cells

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Science China Chemistry 1994年第3期37卷 310-318页

作者：张宏权李风知俞炜源李秀珍方继明费恩阁黄翠芬 Laboratory of Genetic engineering Institute of Biotechnology Molecular Genetics Center Beijing 100850 PRC Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesBeijing 1000850 PRC Laboratory of Genetic engineering Institute of Biotechnology Molecular Genetics Center Beijing 100850 PRC

Human Pro-Urokinase (Pro-UK) is expressed in CHO-DHFR- cells at high efficiency by co-transfecting the mouse dhfr gene and Pro-UK cDNA under the control of the SV40 late promoter. After gene co-amplification, the product level could reach 2-3 μg/106 cells/24 h in the presence of 5×10-6 mol/ L MTX, and the levels can be further raised to 3. 5-4 μg/106 cells/24 h by PMA superinduction. The copy number of Pro-UK cDNA in the genomes of host cells is about 200-300 copies/cell. The Western blot analysis shows that the recombinant Pro-UK has similar molecular weight to its natural counterpart, and also the amidolytic activity of the product is determined by S-2444 assay.

关键词： human Pro-urokinase cDNA CHO-DHFR cells gene co-transfection gene co-amplification PMA superinduction

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Molecular Markers and Candidate Genes for Thermo-Sensitive Genic Male Sterile in Rice

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Rice science 2019年第3期26卷 147-156,I0008-I0012页

作者： Sudthana KHLAIMONGKHON Sriprapai CHAKHONKAEN Keasinee PITNGAM Khanittha DITTHAB Numphet SANGARWUT Natjaree PANYAWUT Thiwawan WASINANON Chareerat MONGKOLSIRIWATANA Julapark CHUNWONGSE Amorntip MUANGPROM center for Agricultural biotechnology Kasetsart University National center for Genetic engineering and biotechnology National Science and Technology Development Agency Division of genetics Faculty of Liberal Arts and Science Kasetsart University

The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), *** 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, *** marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.

关键词： hybrid rice thermo-sensitive genic male sterility insertion/deletion simple sequence repeat marker-assisted selection

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Nitric Oxide Signaling in Plant Responses to Abiotic Stresses

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Journal of Integrative Plant Biology 2008年第10期50卷 1238-1246页

作者： Weihua Qiao Liu-Min Fan Peking-Yale Joint center for Plant Molecular genetics and Agro-biotechnology National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 100871 China

Nitric oxide （NO） plays important roles in diverse physiological processes in plants. NO can provoke both beneficial and harmful effects, which depend on the concentration and location of NO in plant cells. This review is focused on NO synthesis and the functions of NO in plant responses to abiotic environmental stresses. Abiotic stresses mostly induce NO production in plants. NO alleviates the harmfulness of reactive oxygen species, and reacts with other target molecules, and regulates the expression of stress responsive genes under various stress conditions.

关键词： abiotic stress H2O2 nitric oxide reactive oxygen species signal transduction.

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Association of p53/p21 expression with cigarette smoking and prognosis in esophageal squamous cell carcinoma patients

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World Journal of Gastroenterology 2010年第39期16卷 4958-4967页

作者： Noushin Taghavi Firouzeh Biramijamal Masoud Sotoudeh Omeed Moaven Hooman Khademi Mohammad Reza Abbaszadegan Reza Malekzadeh Department of Medical genetics National Institute of Genetic Engineering and Biotechnology Digestive Disease Research center Tehran University of Medical SciencesShariati HospitalNorth Karegar Ave Division of Human genetics Immunology Research CenterAvicenna Research InstituteMashhad University of Medical Sciences

factors,such as cigarette smoking,in esophageal squamous cell carcinoma(ESCC)in northeastern Iran,a region with a high incidence of ***:The expression of p53 and p21 proteins was investigated immunohistochemically in tumor tissue from 80 ESCC patients and in 60 available paraffinembedded blocks of adjacent normal specimens from the cases,along with normal esophageal tissue from 80 healthy ***:Positive expression of p53 protein was detected in 56.2%(45/80)of ESCC cases,and in none of the normal esophageal tissue of the control group(P<0.001).Furthermore,73.8%(59/80)of ESCC cases and 43.8%(35/80)of controls had positive expression of p21 protein(P<0.001).Cigarette smoking was significantly associated with p53 over-expression in ESCC cases(P=0.010,OR=3.64;95%CI:1.32-10.02).p21 over-expression was associated with poorer clinical outcome among the ESCC patients(P=0.009).CONCLUSION:Over-expression of p53 in association with cigarette smoking may play a critical role in ESCC carcinogenesis among this high-risk population of northeastern ***,p21 over-expression was found to be associated with poor prognosis,specifically in the operable ESCC patients.

关键词： Esophageal squamous cell carcinoma p53 p21 Immunohistochemistry Survival Smoking

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Two cases of variant late infantile ceroid lipofuscinosis in Jordan

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World Journal of Clinical Cases 2019年第2期7卷 203-208页

作者： Omar Nafi Bashar Ramadan Olaf Riess Rebecca Buchert Tawfiq Froukh Department of Pediatrics Faculty of Medicine Mutah University Institute of Medical genetics and Applied Genomics Rare Disease Center University of Tübingen Department of biotechnology and Genetic engineering Philadelphia University

BACKGROUND Late infantile ceroid lipofuscinosis is a rare neurodegenerative disorder that appears between the ages of 2 and 4 years and is difficult to diagnose. In this report we present two sisters with this condition, and the clinical course consisted of delayed developmental skills initially and later regression of previously acquired skills. The cases were initially considered as childhood disintegrative disorder(CDD); however, when whole exome sequencing(WES) genetic testing was done, they proved to be variant late infantile ceroid lipofuscinosis. This is the first report from *** SUMMARY Clinical presentation included developmental delay and initially speech delay,followed by lose of sphincter control. Motor development was normal until 4 years of age, then they developed ataxia(fear of going downstairs) and weakness while walking. Atonic and myoclonic seizures become intractable, and this was followed by inability to stand or sit and loss of expressive language. In addition to complete blood count test, liver function test, kidney function test, serum electrolyte test, and blood sugar test, serum amino acid profile, B12 level test,thyroid function test, and a brain computed tomography scan were also *** electroencephalogram showed a generalized spike and wave pattern, and magnetic resonance imaging showed little to no abnormalities. After dealing with the cases as CDD, WES testing proved a final diagnosis of variant late infantile ceroid lipofuscinosis. Current treatment is anti-epileptic drugs and supportive care at home, and they are now in vegetative *** This report highlights the importance of WES for the identification of genetic diseases, especially neurodegenerative disorders.

关键词： Ceroid lipofuscinosis Childhood disintegrative disorder Lysosomal storage disorders Neurodegenerative disorders Variant late infantile Case report

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Function identification of miR159a,a positive regulator during poplar resistance to drought stress

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Horticulture Research 2023年第12期10卷 120-136页

作者： Tiantian Fu Chun Wang Yuzhang Yang Xiaoqian Yang Jing Wang Lichun Zhang Zeqi Wang Yanwei Wang State Key Laboratory of Tree genetics and Breeding National Engineering Research Center of Tree Breeding and Ecological RestorationKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationThe Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland AdministrationCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijing 100083China

Drought seriously affects the growth and development of ***159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress ***,studies of its function in woody plants are still ***,the expression of miR159a was significantly upregulated after drought treatment in poplar,and the overexpression of miR159a(OX159a)significantly reduced the open area of the stomata and improved water-use efficiency in *** drought treatment,OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type *** was the target gene of miR159a,as verified by psRNATarget prediction,RT-qPCR,degradome sequencing,and 5′rapid amplification of cDNA ends(5′RACE).Additionally,miR159a-short tandem target mimic suppression(STTM)poplar lines showed increased sensitivity to drought *** analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite ***,drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a *** investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area,increasing the number and total area of xylem vessels,and enhancing water-use efficiency,and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.

关键词： poplar breeding drought

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Expression and inhibitory activity analysis of a 25-kD Bowman-Birk protease inhibitor in rice

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Chinese Science Bulletin 2006年第1期51卷 54-62页

作者： CHEN Jun MAO Shengji XlE Yang CAO Zhongren ZHANG Yan LIU jing CHEN Zhangliang QU Lijia GU Hongya Peking-Yale Joint center for Plant Molecular genetics and Agro-biotechnology National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 100871 China National Plant Gene Research center (Beijing) Beijing 100101 China

Rice Bowman-Birk inhibitors (RBBI), with one (8 kD) or two homologous domains (16 kD), were found to be effective trypsin inhibitors in vitro. In this study, we demonstrate that the 25-kD protein corresponding to the three-domain RBBI indeed ex- ists in rice in planta, and that the RBBIs are regulated by development and wounding. We also found by inhibitory activity assay that the 3:13 disulfide bond, but not the 4:5 disulfide bond, suppresses the tryp- sin-inhibitory activity, and the D3 domain of RBBI3-1 has no inhibitory activity against trypsin, chymotryp- sin, paparin or subtilisin. Mutation analyses showed that conversion from Lys to Leu or Tyr in the N-terminal P1 site in D1 domain did not create chy- motrypsin-inhibitory activity, suggesting that the structure of the reactive loop in D1 domain hinder the new inhibitory specificity at P1 site, and the chy- motrypsin-inhibitory activity might need the participa- tion of other structures, e.g. 3:13 disulfide bond.

关键词：水稻 RBBI 双硫键胰凝乳蛋白酶胰岛素

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Transcription control engineering and applications in synthetic biology

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Synthetic and Systems biotechnology 2017年第3期2卷 176-191页

作者： Michael D.Engstrom Brian F.Pfleger genetics-biotechnology center University of Wisconsin-Madison School of Medicine and Public HealthUSA Department of Chemical and Biological engineering University of Wisconsin-Madison College of EngineeringUSA Microbiology Doctoral Training Program University of Wisconsin-MadisonUSA

In synthetic biology,researchers assemble biological components in new ways to produce systems with practical *** of these practical applications is control of the flow of genetic information(from nucleic acid to protein),*** *** is critical for optimizing protein(and therefore activity)levels and the subsequent levels of metabolites and other cellular *** central dogma of molecular biology posits that information flow commences with transcription,and accordingly,regulatory tools targeting transcription have received the most attention in synthetic *** this mini-review,we highlight many past successes and summarize the lessons learned in developing tools for controlling *** particular,we focus on engineering studies where promoters and transcription terminators(cis-factors)were directly engineered and/or isolated from DNA *** also review several well-characterized transcription regulators(trans-factors),giving examples of how cis-and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various ***,we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic *** most of our mini-review focuses on the well-characterized bacterium Escherichia coli,we also provide several examples of the use of transcription control engineering in non-model *** approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

关键词： Promoter Transcription Synthetic biology Bacteria Termination Metabolic engineering

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Molecular Studies on Heat Shock Protein 70 Gene （Hsp70） Using ClustalW Multiple Sequence Alignment Analysis

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Journal of Life Sciences 2010年第6期4卷 1-8页

作者： Mohamed A. Ezz Mohamed H. Soliman Abd Alkader Y. Gamal El-Din Aly Z.E. Abdelsalam Molecular genetics Lab Biotechnology College Misr University for Science and Technology 6th of October City October 12451 Egypt Department of genetics Faculty of Agriculture Cairo University Giza 12613 Egypt a in shams center for genetics engineering and biotechnology Faculty of Agriculture Ain Shams University Cairo 11241 Egypt

Degenerate primers are particularly useful in amplifying homologous genes from different organisms. This paper describes a method for designing degenerate primers for a given multiple alignment of DNA sequences of Hsp70 gene family using ClustalW algorithm. The authors used an in silico approach to find a homology between more than one accession numbers of DNA sequences, X67711.2 was for Oryza sativa Hsp70, AY372071.1 was for Nicotiana tabacum Hsp70 and L41253.2 was for Lycopersicon esculentum Hsc70. The three accession numbers which were retrieved by the BLASTn program depend on their expected value （E-value）. Multiple sequence alignment was performed by ClustalW algorithm to produce a conserved blocks and determine the consensus region which had been used to produce the forward and reverse primer by the primer select module of DNAStar Lasergene V7 and In-Silco PCR module of FASTPCR program ver.4.0.8 was performed to detect the melting temperatures （Tm） and predict the PCR product size, The results of designed degenerate primer showed that there was a homology found between the designed primers and the DNA templates for the three accession numbers with at least 80% identity. The result of degenerate PCR showed that the three bands of the amplified PCR products of the three accession numbers were detected at the same molecular weight of marker （400 bp） with a difference about 15 pb compared to the in silco PCR product （385 pb）. In conclusion, this study focused on the importance of using the clustalW algorithm for designing the degenerate primer.

关键词： ClustalW tool degenerate PCR different melting temperatures In-Silico PCR.

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