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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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Maximizing biomass utilization: An integrated strategy for coproducing multiple chemicals

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Journal of Energy Chemistry 2025年第1期100卷 180-191页

作者： Byeongchan Ahn Sua Jo Jonggeol Na J.Jay Liu Young-Ju Kim Wangyun Won Department of Chemical and Biological Engineering Korea University Department of Chemical Engineering (Integrated process) Kyung Hee University Department of Chemical Engineering and Materials Science Ewha Womans University Department of Chemical Engineering Pukyong National University Resources Engineering plant Research Department Korea Institute of Geoscience and Mineral Resources

Lignocellulosic biomass is one of the viable solutions to alleviate the global warming. However, the limited utilization of biomass majorly focused on cellulose and hemicellulose restricts the economic and environmental feasibilities. To cope with this issue, we proposed an integrated process of co-producing 1,6-hexanediol（1,6-HDO） with tetrahydrofuran and adipic acid from biomass, referred to as Strategy A. To compare the impacts of lignin upgrading and feedstock, Strategy B, which co-produces tetrahydrofuran alone, and Strategy C, which is the traditional route to produce 1,6-HDO from fossil fuels, were used. Heat networks are also designed to reduce operating costs and indirect carbon emissions due to energy consumption, saving 87% and 83% of the heat and cooling requirements, respectively, in Strategy A. The market competitiveness of Strategy A was evaluated by determining the minimum selling price through techno-economic analysis, and sustainability was thoroughly investigated by quantifying the environmental impacts through both midpoint and endpoint life-cycle assessments（LCAs）.Strategy A was found to be the most favorable both economically（USRDSCHARDOLLAR3,402/ton） and environmentally（-26.9 kg CO2eq.）. This indicates that lignin valorization is not only economically but also environmentally preferred. Finally, changes in economic and environmental feasibilities depending on economic, process, and environmental parameters were investigated using sensitivity and uncertainty analyses. The results of these analyses provide valuable insight into bio-based chemical production.

关键词： Carbon capture and utilization

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Unraveling the origins of PGY-sRNA-6,BZL-sRNA-20,and XKC-sRNA-h3

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Science China Life Sciences 2025年

作者： Shanfa Lu State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical College Engineering Research Center of Chinese Medicine Resource Ministry of Education

Dear Editor,The regulatory role of herbal sRNAs in humans and animals is an interesting research ***,current evidence is insufficient to conclude that herbal sRNAs are novel precision medicines.I previously showed that HJT-sRNA-m1-HJT-sRNA-m8,identified as herbal sRNAs previously (Du et al.,2019),may be derived from humans and/or animals(Lu,2023).To minimize errors during herbal sRNA analysis,I provided a list of matters needing special attention and proposed problem-solving solutions for researchers working on sRNA cross-kingdom regulation (Lu,2023).

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Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

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Science China Chemistry 2025年第1期68卷 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao Key Laboratory of Phytochemistry and Natural Medicines (Chinese Academy of Sciences) Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences Lab of Computational Chemistry and Drug Design State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen Bay Laboratory State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University State Key Laboratory of Functions and Applications of Medicinal plants Guizhou Medical University Molecular Biology Experimental Center Germplasm Bank of Wild Species in Southwest China Kunming Institute of Botany Chinese Academy of Sciences Yunnan Key Laboratory for Wild plant Resources Kunming Institute of Botany Chinese Academy of Sciences Research Unit of Chemical Biology of Natural Anti-Virus Products Chinese Academy of Medical Sciences

In the intricate process of natural product biosynthesis, a metabolon can enhance metabolic flux by associating sequential enzymes. A fungal metabolon, comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G, is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide B. Using notoamide E as a substance, Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation, followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium unit. Subsequently,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol rearrangement. This provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词： metabolon Diels-Alder reaction semipinacol rearrangement biosynthesis notoamides spiro polycyclic alkaloids

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Quantitative analysis of the interaction of heterologous viruses with Plum pox virus in C5 HoneySweet transgenic plums

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Journal of Integrative Agriculture 2019年第10期18卷 2302-2310页

作者： Khushwant Singh Tereza Neubauerová Jiban Kumar Kundu plant Virus and Vector Interactions Group Division of Crop Protection and Plant Health Crop Research Institute

Stone fruits are an important crop in most parts of the world and are heavily challenged by several viruses including Plum pox virus (PPV), Prune dwarf virus (PDV), Prunus necrotic ringspot virus (PNRSV), and Apple chlorotic leaf spot virus (ACLSV). We validated the PPV resistance in C5 plum plants (commercially known as HoneySweet) grown in the Czech Republic for more than 16 years in a field trial experiment under natural environmental conditions. We quantified single (PPV-Rec) and mixed viruses (PPV-Rec+ACLSV, PPV-Rec+PDV and PPV-Rec+ACLSV+PDV) in C5 transgenic plums inoculated for the period 2016 to 2018. The accumulation of PPV-Rec was high (~5.43E+05 copies) compared with that of ACLSV (~8.70E+04 copies) in the inoculated graft of C5 transgenic plants. Leaves close to the inoculum sources showed a differential level of virus titre in single and mixed infections (~10 to ~5×10^2 copies). C5 plants with permanent virus pressure showed 103- to 105-fold fewer copies of viruses than those of the inoculated graft. We observed high accumulation of conserved miRNAs such as miR167, miR69 and miR396 in C5 plants co-infected with PPV, ACLSV and PDV that are associated with its resistance against viruses. Overall, i) C5 transgenic plums showed high resistance to PPV infection, and a low level (~32 copies) of PPV only accumulated in some grafted plants, ii) high accumulation of PPV was found in inoculated grafts in single PPV infection and mixed infections, iii) heterologous virus infection sustained by ACLSV or PDV did not suppress PPV resistance, and iv) high and low conserved microRNAs accumulated in C5 plants.

关键词： PPV PDV ACLSV C5 HoneySweet resistance

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Morphological and molecular characterizations of cereal cyst nematode Heterodera avenae Wollenweber, 1924 from the Czech Republic

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Journal of Integrative Agriculture 2017年第3期16卷 532-539页

作者： Shesh Kumari Division of Crop Protection and plant health Crop Research Institute Prague 16106 Czech Republic

The cereal cyst nematode,Heterodera avenae Wollenweber,1924,is a major pest of cereal crops throughout the world and causes serious yield losses,especially of *** studies have shown that this species is widely distributed in the Czech *** this study,seven populations of *** were molecularly studied,and one population was morphologically *** regions（18S,28S,and internal transcribed spacer 1）of ribosomal DNA were sequenced and the analysis of the 18S gene of six populations did not reveal any variation,whereas the internal transcribed spacer 1and 28S sequences of six populations differed by only two nucleotides from a population in？*** and quick identification of cereal cyst nematodes is important for effective control measures and ribosomal sequence analyses of seven populations in this study will be useful in future phylogenetic studies of Heterodera *** in the Czech Republic.

关键词： Heterodera avenae PCR ribosomal DNA sequencing nematode

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Unveiling phosphofructokinase as the key target: an innovative strategy combining pull-down assays with optical imaging for snail-killing mechanism exploration

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Science China Chemistry 2025年

作者： Yuxun Lu Weisi Wang Le Yu Yuqiang Zhao Ying Chen Yunhai Guo Bingrong Luo Yuhua Liu Shizhu Li Liping Duan Ying Zhou Yunnan Characteristic plant Extraction Laboratory College of Chemical Science and Technology Yunnan University College of Biological and Chemical Engineering Guangxi University of Science and Technology National institute of Parasitic Diseases Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research)NHC Key Laboratory of Parasite and Vector Biology WHO Collaborating Centre for Tropical Diseases National Center for International Research on Tropical Diseases School of Chemistry and Environment Yunnan Minzu University Dali institute of Schistosomiasis Control

The Pomacea canaliculata, also known as apple snail, is an invasive species in China, posing a serious threat to agricultural production and public health. To prevent its rampant infestation, we developed a highly efficient snail-killing lead compound, 1-(4-chlorophenyl)-3-(pyridin-3-yl)urea (PBQ). However, the killing mechanism of PBQ remains unclear. To elucidate this, two novel compounds, B-PBQ and J-PBQ, were developed through structural modification of PBQ and were used, through both protein pull-down assay and confocal laser scanning microscopy imaging, to identify and confirm that phosphofructokinase(PFK) in the apple snail is the primary target protein of PBQ. Further studies revealed that PBQ successfully inhibits the activity,content, and expression of PFK in apple snail, disrupting the glycolysis pathway and leading to abnormal energy *** disruptions impair the snail’s tolerance to low oxygen, resulting in its efficient eradication. These findings offer a promising direction for developing next-generation PFK-targeted snail-killing pesticides. Furthermore, the strategy of combining pull-down assays with optical imaging used in this work provides a novel approach for the exploration of mechanisms of other pesticide candidates.

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Diapause development in early and late emerging phenotypes of Delia floralis

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Insect Science 2014年第1期21卷 103-113页

作者： Tor J. Johansen Richard Meadow Arctic Agriculture and Land Use Division Bioforsk - Norwegian Institute for Agricultural and Environmental Research Tromsm plant health and plant Protection Division Bioforsk - Norwegian Institute for Agricultural and Environmental Research As Norway

The turnip fly, Delia floralis Fall6n （Diptera： Anthomyiidae） is an important insect pest of brassica vegetable crops in the holarctic region. Different populations have strongly varying temperature requirements for fly emergence, a challenge for accurate prediction of activity. This study focused on diapause development in one early and one late emerging phenotype. The physiological state after various treatments was deduced from emergence data. Our results showed a slow diapause progression at chilling conditions for both populations and diapause ended about 7 months after pupae were formed for the early population. For the late population held at 4℃ diapause did not end, no matter how long the duration of chilling. These pupae required a period with elevated temperatures above 6~C to continue development. At constant non-chilling conditions （18℃） from the time pupae were formed both populations completed diapause most rapidly. These results indicate that chilling delayed, rather than accelerated development and was not a prerequisite for diapause development. For post-diapause, results indicated a linear relationship between rate of development and temperature within the range of 6-18℃and a theoretical base temperature for development of about 2℃ for both populations. In conclusion, D. floralis pupae are in diapause throughout a long winter period, and delayed emergence of the late population appears to be caused by prolonged diapause regulated by a developmental temperature threshold. The study has added information on the biology of turnip fly populations, a prerequisite for improved pest control.

关键词： brassica chilling emergence hibernation quiescence

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The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

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Journal of Integrative plant Biology 2018年第12期60卷 1127-1153页

作者： Jochen Kumlehn Janine Pietralla Goetz Hensel Michael Pacher Holger Puchta plant Reproductive Biology Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Botanical institute Molecular Biology and Biochemistry Karlsruhe Institute of Technology

Since the discovery that nucleases of the bacterial CRISPR(clustered regularly interspaced palindromic repeat)-associated(Cas) system can be used as easily programmable tools for genome engineering,their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction,resulting in mutations by non-homologous recombinatr e-tion. Strategies for performing such experiments à from Rthe design of guide RNA to the use of different transformation technologies à are evaluated. Furtherweive-more, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNAbinding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.

关键词： From efficient gene editing for crop breeding to plant synthetic biology The CRISPR/Cas revolution continues

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Rhizobial infection triggers systemic transport of endogenous RNAs between shoots and roots in soybean

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Science China(Life Sciences) 2020年第8期63卷 1213-1226页

作者： Chen Zhang Meifang Qi Xiaxia Zhang Qi Wang Yanjun Yu Yijing Zhang Zhaosheng Kong State Key Laboratory of plant Genomics Institute of MicrobiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China Shanghai institute of plant Physiology and Ecology Chinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China

Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called *** have shown that abiotic and biotic stresses alter the profile of gene expression and transcript mobility in ***,little is known about the systemic transport of RNA between roots and shoots in response to rhizobial infection on a genome-wide scale during the formation of legume-rhizobia *** our study,we found that two soybean(Glycine max)cultivars,Peking and Williams,show a high frequency of single nucleotide polymorphisms;this allowed us to characterize the origin and mobility of transcripts in hetero-grafts of these two *** identified 4,552 genes that produce mobile RNAs in soybean,and found that rhizobial infection triggers mass transport of m RNAs between shoots and roots at the early stage of *** majority of these mRNAs are of relatively low abundance and their transport occurs in a selective manner in soybean ***,the mRNAs that moved from shoots to roots at the early stage of nodulation were enriched in many nodule-related responsive ***,the transcripts of many known symbiosis-related genes that are induced by rhizobial infection can move between shoots and *** findings provide a deeper understanding of endogenous RNA transport in legume-rhizobia symbiotic processes.

关键词： symbiosis nodulation systemic transport of RNAs soybean rhizobia

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