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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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Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice

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Journal of Integrative Plant Biology 2024年第7期66卷 1440-1458页

作者： Yingchun Han Qianfeng Hu Nuo Gong Huimin Yan Najeeb Ullah Khan Yanxiu Du Hongzheng Sun Quanzhi Zhao Wanxi Peng Zichao Li Zhanying Zhang Junzhou Li henan key laboratory of rice molecular breeding and high efﬁciency production College of AgronomyHenan Agricultural UniversityZhengzhou 450046China Beijing key laboratory of Crop Genetic Improvement College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China rice Industrial Technology Research Institute Guizhou UniversityGuiyang 550025China School of Forestry Henan Agricultural UniversityZhengzhou 450046China

Grain yield is determined mainly by grain number and grain *** this study,we identified and characterized MORE GRAINS1(MOG1),a gene associated with grain number and grain weight in rice(Oryza sativa L.),through map-based *** of MOG1 increased grain yield by 18.6%-22.3%under field *** determined that MOG1,a bHLH transcription factor,interacts with OsbHLH107 and directly activates the expression of LONELY GUY(LOG),which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1(EXPLA1),positively regulating grain number per panicle and grain *** variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation,leading to functional *** analysis revealed that Hap-HNW,which results in a greater number and heavier grains,has undergone strong selection but has been poorly utilized in modern lowland rice *** summary,the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway,thereby increasing grain number and grain *** findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.

关键词： grain number grain weight MOG1 natural variation rice

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Bacterial indole-3-propionic acid inhibits macrophage IL-1β production through targeting methionine metabolism

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Science China Life Sciences 2025年

作者： Ziyi Han Jian Fu Aiyan Gong Wenkai Ren State key laboratory of Livestock and Poultry breeding College of Animal Science South China Agricultural University Animal Disease-resistant Nutrition Key Laboratory of Sichuan Province Sichuan Agricultural University China Institute of Veterinary Drug Control

The gut microbiota plays key roles in host health by shaping the host immune responses through their metabolites, like indole derivatives from tryptophan. However, the direct role of these indole derivatives in macrophage fate decision and the underlying mechanism remains unknown. Here, we found that bacterial indole-3-propionic acid(IPA) downregulates interleukin-1beta(IL-1β) production in M1 macrophages through inhibition of nuclear factor-kappa B(NF-κB) signaling. Mechanistically, IPA binds specifically with methionine adenosyltransferase 2A(MAT2A) to promote S-adenosylmethionine(SAM) synthesis, which facilitates the DNA methylation of ubiquitin-specific peptidase 16(USP16, a deubiquitinase), and in turn promotes Toll-like receptor 4(TLR4) ubiquitination and NF-κB inhibition. Furthermore,IPA administration attenuates sepsis in mouse models induced by lipopolysaccharides(LPS), showcasing its potential as a microbial-derived adjunct in alleviating inflammation. Collectively, our findings reveal a newly found microbial metabolite-immune system regulatory pathway mediated by IPA.

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AtRKD5 inhibits the parthenogenic potential mediated by AtBBM

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Journal of Integrative Plant Biology 2024年第7期66卷 1517-1531页

作者： Qiyan Liu Dongfen Han Denghu Cheng Jinfan Chen Shujuan Tian Jiafa Wang Man Liu Li Yuan State key laboratory of Crop Stress Resistance and high‐efﬁciency production College of HorticultureNorthwest A&F UniversityYangling 712100China

Parthenogenesis,the development of unfertilized egg cells into embryos,is a key component of ***(BABY BOOM),a crucial regulator of embryogenesis in Arabidopsis,possesses the capacity to shift nutritional growth toward reproductive ***,the mechanisms underlying AtBBM-induced parthenogenesis remain largely unexplored in dicot *** findings revealed that in order to uphold the order of sexual reproduction,the embryo-specific promoter activity of AtBBM as well as repressors that inhibit its expression in egg cells combine to limiting its ability to induce ***,AtRKD5,a RWPRK domain-containing(RKD)transcription factor,binds to the 3'end of AtBBM and is identified as one of the inhibitory factors for AtBBM expression in the egg *** the atrkd5 mutant,we successfully achieved enhanced ectopic expression of AtBBM in egg cells,resulting in the generation of haploid offspring via parthenogenesis at a rate of 0.28%.Furthermore,by introducing chimeric Arabidopsis and rice BBM genes into the egg cell,we achieved a significant 4.6-fold enhancement in haploid induction through the atdmp8/9 *** findings lay a strong foundation for further exploration of the BBM-mediated parthenogenesis mechanism and the improvement of haploid breeding efficiency mediated by the dmp8/9 mutant.

关键词： AtBBM atdmp AtRKD5 haploid induction parthenogenesis

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Fine-tuning the spatial allocation of phytohormones for smart canopy, smart breeding, and smart agriculture

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Science China Life Sciences 2025年第1期68卷 309-310页

作者： Tao Zhou Lin Li National key laboratory of Crop Genetic Improvement Huazhong Agricultural University HuBei HongShan laboratory

The dual challenges of global climate change and population growth have increased demand for higher crop yields per unit area. The innovative technology of smart agriculture aims to synergize breeding, cultivation, and production through the application of biological and informatics technologies. Historically, the “Green Revolution” introduced semidwarf varieties of certain key crops by utilizing mutations affecting gibberellin pathways, which significantly increased planting densities and yields.

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Transcript Profiling Reveals Abscisic Acid,Salicylic Acid and Jasmonic-Isoleucine Pathways Involved in high Regenerative Capacities of Immature Embryos Compared with Mature Seeds in japonica rice

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rice science 2018年第4期25卷 227-234页

作者： XIAO Kaizhuan MAO Xiaohui WANG Yingheng WANG Jinlan WEI Yidong CAI Qiuhua XIE Hua'an ZHANG Jianfu College of Life Sciences Fujian Normal UniversityFuzhou 350108China rice Research Institute Fujian Academy of Agricultural SciencesFuzhou 350019China key laboratory of Germplasm Innovation and molecular breeding of Hybrid rice for South China Ministry of Agriculture/Incubator of National Key Laboratory of Fujian Germplasm Innovation and Molecular Breeding Between Fujian and Ministry of Sciences&Technology/Fuzhou BranchNational Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding/Base of South ChinaState Key Laboratory of Hybrid Rice/National Rice Engineering LaboratoryFuzhou 350003China

Induced pluripotent cell mass plays a role in genetic transformation mediated by Agrobacterium. Mature seeds are more recalcitrant to the induction of suitable calli than immature embryos in rice, but the exact molecular mechanisms involved remain elusive. In this study, the morphological structure of calli induced from mature seeds and immature embryos were observed under a scanning electron microscope using a paraffin embedded technique. Meanwhile, a total of 2 173 up- and down-regulated genes were identified in calli induced from mature seeds and immature embryos by RNA-seq technique and furtherly confirmed by quantitative real-time PCR. The results revealed the remarkable morphological differences in calli induced from mature seeds and immature embryos, and plant hormone signal transduction and hormone biosynthesis pathways, such as abscisic acid, salicylic acid and jasmonic-isoleucine, were found to play roles in somatic embryogenesis. This study provided comprehensive gene expression sets for mature seeds and immature embryos that were served as an important platform resource for further functional studies in plant embryogenesis.

关键词： callus immature embryo mature seed japonica rice RNA sequence hormone

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Phenotype of rice Floury Endosperm Mutant flo7 and Fine Mapping of Mutated Gene

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rice science 2015年第4期22卷 162-170页

作者： SHENG Zhong-hua FANG Peng-fei LI San-feng JIAO Gui-ai XIE Li-hong HU Pei-song TANG Shao-qing WEI Xiang-jin State key laboratory of rice Biology/key laboratory of rice Biology and Genetic breeding of Ministry of Agriculture China National Rice Research Institute

The major storage substance in rice endosperm is starch, which accounts for 80% of dry matter weight. In this study, rice mutant flo7, selected from the progeny of Nipponbare＇s tissue culture, displayed floury and opaque endosperm. Compared with its corresponding wild type （WT） Nipponbare, the mutant rio7 produced longer, narrower, thinner and lighter grains. The levels of glucose, fructose and sucrose in the mutant flo7 endosperm were higher than those in the WT endosperm, whereas the protein content was not affected. With respect to both amylose content and gel consistency, the mutant flo7 was lower than WT, but its alkali value was higher. Scanning electron microscopic examinations showed that the endosperm of the mutant flo7 contained irregular, loosely packed and compound starch granules. Genetic analysis indicated that the mutant phenotype was determined by a single recessive nuclear gene The flo7 locus was mapped to a region on the long arm of chromosome 12, within a 95.1 kb interval defined by the markers C2-11 and C5-15. There are 13 open reading frames in the mapping interval. Transcription profiling of the developing grains showed that a number of genes involved in starch synthesis were affected differently in the mutant flo7.

关键词： flo7 floury endosperm starch fine mapping rice mutant

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Determination of Heterotic Groups and Heterosis Analysis of Yield Performance in indica rice

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rice science 2018年第5期25卷 261-269页

作者： WANG Yingheng CAI Qiuhua XIE Hongguang WU Fangxi LIAN Ling HE Wei CHEN Liping XIE Hua'an ZHANG Jianfu College of Crop Sciences Fujian Agriculture and Forestry University Fuzhou 350002 China rice Research Institute Fujian Academy of Agricultural Sciences Fuzhou 350019 China key laboratory of Germplasm Innovation and molecular breeding of Hybrid rice for South China Ministry of Agriculture / Fuzhou Branch National Rice Improvement Center / Fujian Engineering Laboratory of Crop Molecular Breeding / Fujian Key Laboratory of Rice Molecular Breeding Fuzhou 350003 China Incubator of National key laboratory of Fujian Germplasm Innovation and molecular breeding Between Fujian and Ministry of Sciences & Technology Fuzhou 350003 China National rice Engineering laboratory Fuzhou 350003 China

To compare the heterosis levels among various groups of parental lines used extensively in China, identify foundational heterotic groups in parental pools and understand the relationship between genetic distance and heterosis performance, 16 parental lines with extensive genetic variation were selected from various sub-groups, and 39 hybrid combinations were generated and evaluated in Fujian and Hainan Provinces of China. The main results were as follows：（1） The 16 parental lines can be grouped into 7 sub-groups consisting of 1 maintainer sub-group and 6 restorer sub-groups; （2） Mean grain yield of the restorer lines was higher than that of the maintainer lines, and mean yield of parental lines was higher than that of the hybrid combinations; （3） The two best heterotic patterns were II-32A × G5 and II-32A × G6, moreover, the order of restorer sub-groups according to grain yield, from the highest to lowest, was G7, G6, G5, G4, G3 and G2; high specific combining ability values were observed for combinations of II-32A × G5, II-32A × G6 and Tianfeng A × G7; （4） Hybrid combinations derived from II-32A crossed with 13 restorer lines had higher yield trait values （mid-parent heterosis, better-parent heterosis, standard heterosis over check and specific combining ability） than any other combinations; （5） Genetic distance was positively correlated with panicle number, grain length and length-to-width ratio （P 〈 0.05） and negatively correlated with grain width, grain yield, seed-setting rate, as well as mid-parent heterosis, standard heterosis over check, and specific combining ability for grain yield （P 〈 0.01）. These heterotic groups and patterns and their argonomic traits will provide useful information for future hybrid rice breeding programs.

关键词： rice heterosis heterosis group general combine ability specific combine ability genetic distance

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OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in rice

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rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo State key laboratory of rice Biology and breeding China National Rice Research InstituteHangzhou 310006China Jiangsu key laboratory of Crop Genetics and Physiology/key laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu key laboratory of Crop Genomics and molecular breeding/Jiangsu Co-Innovation Center for Modern production Technology of Grain Crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

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NRL3 Interacts with OsK4 to Regulate Heading Date in rice

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rice science 2022年第3期29卷 237-246页

作者： CHEN Wei CAI Yicong Shakeel AHMAD WANG Yakun AN Ruihu TANG Shengjia GUO Naihui WEI Xiangjin TANG Shaoqing SHAO Gaoneng JIAO Guiai XIE Lihong HU Shikai SHENG Zhonghua HU Peisong key laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/Collaboration Center for Double-Season Rice Modernization ProductionJiangxi Agricultural University/Research Center of Super Rice Engineering and TechnologyJiangxi ProvinceNanchang 330045China State key laboratory of rice Biology/key laboratory of rice Biology and breeding Ministry of Agriculture and Rural Affairs/China National Rice Improvement Center/China National Rice Research InstituteHangzhou 310006China

NRL3 is essential for the growth and development of rice *** this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight *** yeast two-hybrid and the bimolecular fluorescence complementation proved that NRL3interacts with OsK4,a Snf1-related ***4 localized to the nucleus and expressed in various rice *** rhythmic expression pattern of Os K4 was similar to NRL3 under long daylight and short daylight ***-out mutants of Os K4 exhibited early heading under long daylight conditions,indicating that it acts as a negative regulator of heading date in ***,the OsK4 mutant under the nrl3 mutant background rescued the late heading phenotype of nrl3 under long daylight conditions,suggesting that Os K4 functions downstream of ***,both NRL3 and Os K4 controlled heading date through regulating the expression of Hd3a and RFT1 *** findings shed light on the heading date regulation in rice and provide a sound theoretical base to improve regional adaptability of rice.

关键词： Oryza sativa heading date NRL3 gene OsK4 gene negative regulator loss function

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