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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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Performance Comparison of Two Efficient Genomic Selection Methods(gsbay & MixP ) applied in Aquacultural Organisms

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Journal of Ocean University of China 2017年第1期16卷 137-144页

作者： SU Hailin LI Hengde WANG Shi WANG Yangfan BAO Zhenmin College of Marine life science Ocean University of China The center for applied Aquatic genomics Chinese Academy of Fishery Sciences

Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

关键词： genomic selection scallop breeding method comparison

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A Proximal Promoter Region of Arabidopsis DREB2C Confers Tissue-specific Expression under Heat Stress

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Journal of Integrative Plant Biology 2012年第9期54卷 640-651页

作者： Jihyun Je Chieun Song Jung Eun Hwang Chae Oh Lim Systems and Synthetic Agrobiotech center and PMBBRC Division of Applied Life Science Gyeongsang National University

The dehydration-responsive element-binding factor 2C （DREB2C） is a member of the CBF/DREB subfamily of proteins, which contains a single APETALA2/Ethylene responsive element-binding factor （AP2/ERF） domain. To identify the expression pattern of the DREB2C gene, which contains multiple transcription cis-regulatory elements in its promoter, an approximately 1.4 kb upstream DREB2C sequence was fused to the β-glucuronidase reporter gene （GUS） and the recombinant p1244 construct was transformed into Arabidopsis thaliana （L.） Heynh. The promoter of the gene directed prominent GUS activity in the vasculature in diverse young dividing tissues. Upon applying heat stress （HS）, GUS staining was also enhanced in the vasculature of the growing tissues. Analysis of a series of 5＇-deletions of the DREB2C promoter revealed that a proximal upstream sequence sufficient for the tissue-specific spatial and temporal induction of GUS expression by HS is localized in the promoter region between -204 and -34 bps relative to the transcriptional start site. Furthermore, electrophoretic mobility shift assay （EMSA） demonstrated that nuclear protein binding activities specific to a -120 to -32 bp promoter fragment increased after HS. These results indicate that the TATA-proximal region and some latent trans-acting factors may cooperate in HS-induced activation of the Arabidopsis DREB2C promoter.

关键词： cis-acting elements β-glucuronidase gene expression histochemical assay promoter deletion transgenic plant.

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A Lipidomic Study of the Effects of N-methyl-N′-nitro-N-nitrosoguanidine on Sphingomyelin Metabolism

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Acta Biochimica et Biophysica Sinica 2005年第8期37卷 515-524页

作者： Yun HUANG~(&#) Jing SHEN~# Ting WANG Yan-Ke YU Fanqing E CHEN~1 Jun YANG~* Department of Pathology and Pathophysiology,center for Environmental genomics Zhejiang University School of Medicine,Hangzhou 310031,China ~1 Molecular Biology Branch.life science division,Lawrence Berkeley National Laboratory,University of California at Berkeley,Berkeley,CA 94720,USA Department of Chemistry,Georgia State University.Atlanta,GA 30303.USA Department of Pathology and Pathophysiology Center for Environmental Genomics Zhejiang University School of MedicineHangzhou 310031 China Molecular Biology Branch Life Science Division Lawrence Berkeley National Laboratory University of California at BerkeleyBerkeley CA 94720 USA

Systems biology is a new and rapidly developing research area in which,by quantitativelydescribing the interaction among all the individual components of a cell,a systems-level understanding of abiological response can be ***,it requires high-throughput measurement technologies forbiological molecules,such as genomic and proteomic approaches for DNA/RNA and protein,***,a new concept,lipidomics,which utilizes the mass spectrometry(MS)method for lipid analysis,has been *** this lipidomic approach,the effects of N-methyl-N'-nitro-N-nitrosoguanidine(MNNG)on sphingomyelin metabolism,a major class of sphingolipids,were *** moleculeswere extracted from cells and analyzed by matrix-assisted laser desorption ionization-time of flight *** found that MNNG induced profound changes in sphingomyelin metabolism,including the appearance ofsome new sphingomyelin species and the disappearance of some others,and the concentrations of severalsphmgomyelin species also *** was accompanied by the redistribution of acid sphingomyelinase(ASM),a key player in sphingomyelin *** the other hand,imipramine,an inhibitor of ASM,caused the accumulation of *** also prevented some of the effects of MNNG,as well as theredistribution of *** together,these data suggested that the lipidomic approach is highly effectivefor the systematic analysis of cellular lipids metabolism.

关键词： lipidomics mass spectrometry ceramide sphingomyelin acid sphingomyelinase

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A Survey of the L1 Scheme in the Discretisation of Time-Fractional Problems

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Numerical Mathematics(Theory,Methods and Applications) 2022年第4期15卷 1173-1192页

作者： Martin Stynes applied and Computational Mathematics division Beijing Computational Science Research CenterBeijing 100193China

A survey is given of convergence results that have been proved when the L1 scheme is used to approximate the Caputo time derivative D_(t)^(α)(where 0<α<1)in initial-boundary value problems governed by D_(t)^(α)u−△u=f and similar equations,while taking into account the weak singularity that is present in typical solutions of such *** aspects of these analyses are outlined,such as global and local convergence bounds and the techniques used to derive them,fast implementation of the L1 scheme,semilinear problems,multi-term time derivatives,α-robustness,a posteriori error analysis,and two modified L1 schemes that achieve better *** fifty references are provided in the bibliography,more than half of which are from the period 2019-2022.

关键词： L1 scheme fractional derivative survey

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AluScanCNV2:An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data

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Genes & Diseases 2019年第1期6卷 43-46页

作者： Taobo Hu Si Chen Ata Ullah Hong Xue division of life science Applied Genomics Centre and Centre for Statistical ScienceHong Kong University of Science and TechnologyClear Water BayHong Kong School of Basic Medicine and Clinical Pharmacy China Pharmaceutical UniversityNanjingChina

The usage of next-generation sequencing(NGS)to detect copy number variation(CNV)is widely accepted in cancer *** on an AluScanCNV software developed by us previously,an AluScanCNV2 software has been developed in the present study as an R package that performs CNV detection from NGS data obtained through AluScan,wholegenome sequencing or other targeted NGS *** applications would include the expedited usage of somatic CNVs for cancer subtyping,and usage of recurrent germline CNVs to perform machine learning-assisted prediction of a test subject’s susceptibility to cancer.

关键词： AluScan Bioinformatics Cancer subtyping Cancer predisposition Machine learning

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Genomic alterations in pancreatic cancer and their relevance to therapy

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World Journal of Gastrointestinal Oncology 2015年第10期7卷 250-258页

作者： Erina Takai Shinichi Yachida division of Cancer genomics National Cancer Center Research Institute

Pancreatic cancer is a highly lethal cancer type, for which there are few viable therapeutic options. But, with the advance of sequencing technologies for global genomic analysis, the landscape of genomic alterations in pancreatic cancer is becoming increasingly well understood. In this review, we summarize current knowledge of genomic alterations in 12 core signaling pathways or cellular processes in pancreatic ductal adenocarcinoma, which is the most common type of malignancy in the pancreas, including four commonly mutated genes and many other genes that are mutated at low frequencies. We also describe the potential implications of these genomic alterations for development of novel therapeutic approaches in the context of personalized medicine.

关键词： Pancreatic cancer Genomic alterations Signaling pa

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Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library

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The Crop Journal 2016年第1期4卷 40-47页

作者： Lixia Wang Kyung Do Kim Dongying Gao Honglin Chen Suhua Wang Suk Ha Lee Scott A. Jackson Xuzhen Cheng Institute of Crop science Chinese Academy of Agricultural Sciences center for applied Genetic Technologies University of Georgia Plant genomics and Breeding Institute Seoul National University

Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important *** we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR *** 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung ***, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice b

关键词： Vigna umbellata SSR Distribution and frequency Mapping Primer design

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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.

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The processed C-terminus of AvrRps4 effector suppresses plant immunity via targeting multiple WRKYs

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Journal of Integrative Plant Biology 2024年第8期66卷 1769-1787页

作者： Quang-Minh Nguyen Arya Bagus Boedi Iswanto Hobin Kang Jiyun Moon Kieu Anh Thi Phan Geon Hui Son Mi Chung Suh Eui-Hwan Chung Walter Gassmann Sang Hee Kim division of applied life science(BK21 Four Program) Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 52828Korea Department of life science Sogang UniversitySeoul 04107Korea Department of Plant Biotechnology Korea UniversitySeoul 02841Korea division of Plant science and Technology Christopher S.Bond Life Sciences Center and Interdisciplinary Plant GroupUniversity of MissouriColumbiaMissouri 65211USA division of life science and Research Institute of Molecular Alchemy Gyeongsang National UniversityJinju 52828Korea

Pathogens generate and secrete effector proteins to the host plant cells during pathogenesis to promote virulence and *** the plant carries resistance(R)proteins that recognize pathogen effectors,effector-triggered immunity(ETI)is activated,resulting in a robust immune response and hypersensitive response(HR).The bipartite effector AvrRps4 from Pseudomonas syringae *** has been well studied in terms of avirulence *** planta,AvrRps4 is processed into two *** Cterminal fragment of AvrRps4(AvrRps4^(C))induces HR in turnip and is recognized by the paired resistance proteins AtRRS1/AtRPS4 in ***,we show that AvrRps4^(C)targets a group of Arabidopsis WRKY,including WRKY46,WRKY53,WRKY54,and WRKY70,to induce its virulence ***,AvrRps4^(C)suppresses the general binding and transcriptional activities of immune-positive regulator WRKY54 and WRKY54-mediated ***4^(C)interferes with WRKY54's binding activity to target gene SARD1 in vitro,suggesting WRKY54 is sequestered from the SARD1 promoter by AvrRps4^(C).Through the interaction of Avr Rps4^(C)with four WRKYs,AvrRps4 enhances the formation of homo-/heterotypic complexes of four WRKYs and sequesters them in the cytoplasm,thus inhibiting their function in plant ***,our results provide a detailed virulence mechanism of AvrRps4 through its C-terminus.

关键词： AvrRps4 bacterial effector effector-triggered immunity immune response suppression transcription factor WRKY

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