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Histological and single-nucleus transcriptome analyses reveal the specialized functions of ligular sclerenchyma cells and key regulators of leaf angle in maize

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Molecular Plant 2024年第6期17卷 920-934页

作者： Qibin Wang Qiuyue Guo Qingbiao Shi Hengjia Yang Meiling Liu Yani Niu Shuxuan Quan Di Xu Xiaofeng Chen Laiyi Li Wenchang Xu Fanying Kong Haisen Zhang Pinghua Li Bosheng Li Gang Li state key laboratory of Wheat improvement College of Life SciencesShandong Agricultural UniversityTai’an 271018China Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agriculture Sciences in WeifangWeifangShandong 261325China state key laboratory of Wheat improvement College of AgronomyShandong Agricultural UniversityTai’an 271018China

Leaf angle(LA)is a crucial factor that affects planting density and yield in ***,the regulatory mechanisms underlying LA formation remain largely *** this study,we performed a comparative histological analysis of the ligular region across various maize inbred lines and revealed that LA is significantly influenced by a two-step regulatory process involving initial cell elongation followed by subsequent lignification in the ligular adaxial sclerenchyma cells(SCs).Subsequently,we performed both bulk and single-nucleus RNA sequencing,generated a comprehensive transcriptomic atlas of the ligular region,and identified numerous genes enriched in the hypodermal cells that may influence their specialization into ***,we functionally characterized two genes encoding atypical basic-helix-loop-helix(bHLH)transcription factors,bHLH30 and its homolog bHLH155,which are highly expressed in the elongated adaxial *** analyses revealed that bHLH30 and bHLH155 positively regulate LA expansion,and molecular experiments demonstrated their ability to activate the transcription of genes involved in cell elongation and lignification of *** findings highlight the specialized functions of ligular adaxial SCs in LA regulation by restricting further extension of ligular cells and enhancing mechanical *** transcriptomic atlas of the ligular region at single-nucleus resolution not only deepens our understanding of LA regulation but also enables identification of numerous potential targets for optimizing plant architecture in modern maize breeding.

关键词： planting specialized angle

Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation

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Journal of Integrative Plant Biology 2024年第1期66卷 121-142页

作者： Shuangcheng He Yuanchang Min Zijin Liu Fang Zhi Rong Ma Ankang Ge Shixiang Wang Yu Zhao Danshuai Peng Da Zhang Minshan Jin Bo Song Jianjun Wang Yuan Guo Mingxun Chen state key laboratory for crop Stress Resistance and High‐Efficiency Production National Yangling Agricultural Biotechnology&Breeding CenterShaanxi Key Laboratory of Crop HeterosisCollege of AgronomyNorthwest A&F UniversityYangling 712100China state key laboratory for crop Stress Resistance and High‐Efficiency Production Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYangling 712100China

Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in *** far,the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely ***,we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK(STK)and SEPALLATA3(SEP3),which bridges several key genes to regulate oil accumulation in *** found that STK,highly expressed in the developing embryo,positively regulates seed oil accumulation in Arabidopsis(Arabidopsis thaliana).Furthermore,we discovered that SEP3 physically interacts with STK in vivo and in *** oil content is increased by the SEP3 mutation,while it is decreased by SEP3 *** chromatin immunoprecipitation,electrophoretic mobility shift assay,and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5,SEP3,and SEED FATTY ACID REDUCER 4(SFAR4).Moreover,genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5,SEP3,and ***,we demonstrated that TRANSPARENT TESTA 8(TT8)and ACYL-ACYL CARRIER PROTEIN DESATURASE 3(AAD3)are direct targets of MYB5 during seed oil accumulation in ***,our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3,which fine tunes oil accumulation in seeds.

关键词： seed oil accumulation SEP3 STK transcription factor transcriptional regulation

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

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The crop Journal 2024年第3期12卷 688-697页

作者： Mingdong Zhu Meng Zhang Kunyong Huang Feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei state key laboratory of Rice Biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006ZhejiangChina b state key laboratory of Hybrid Rice Hunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125HunanChina Hunan Provincial key laboratory of Plant Functional Genomics and Developmental regulation College of BiologyHunan UniversityChangsha 410082HunanChina Hubei University Wuhan 430062HubeiChina

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ ***,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice *** 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific *** genes of multiple cell types were expressed in several clusters,suggesting a complex developmental *** genes for signaling by phytohormones such as abscisic acid were highly expressed in specific *** cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain *** expression patterns of genes involved in rapid seed germination,seedling growth,and development were *** findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

关键词： Rice Plumule Single-cell sequencing Regulatory network

Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal transduction

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Journal of Integrative Plant Biology 2024年第5期66卷 973-985页

作者： Qingbiao Shi Ying Xia Na Xue Qibin Wang Qing Tao Mingjing Li Di Xu Xiaofei Wang Fanying Kong Haisen Zhang Gang Li National key laboratory of Wheat improvement College of Life SciencesShandong Agricultural UniversityTai'an 271018China National key laboratory of Wheat improvement College of AgronomyShandong Agricultural UniversityTai'an 271018China

Starch is a major storage carbohydrate in plants and is critical in crop yield and *** synthesis is intricately regulated by internal metabolic processes and external environmental cues;however,the precise molecular mechanisms governing this process remain largely *** this study,we revealed that high red to far-red(high R:FR)light significantly induces the synthesis of leaf starch and the expression of synthesis-related genes,whereas low R:FR light suppress these *** phytochrome B(phyB),the primary R and FR photoreceptor,was identified as a critical positive regulator in this *** of phyB,basic leucine zipper transcription factor ELONGATED HYPOCOTYL5(HY5)was found to enhance starch synthesis,whereas the basic helix-loop-helix transcription factors PHYTOCHROME INTERACTING FACTORs(PIF3,PIF4,and PIF5)inhibit starch synthesis in Arabidopsis ***,HY5 and PIFs directly compete for binding to a shared G-box cis-element in the promoter region of genes encoding starch synthases GBSS,SS3,and SS4,which leads to antagonistic regulation of their expression and,consequently,starch *** findings highlight the vital role of phyB in enhancing starch synthesis by stabilizing HY5 and facilitating PIFs degradation under high R:FR light ***,under low R:FR light,PIFs predominantly inhibit starch *** study provides insight into the physiological and molecular functions of phyB and its downstream transcription factors HY5 and PIFs in starch synthesis regulation,shedding light on the regulatory mechanism by which plants synchronize dynamic light signals with metabolic cues to module starch synthesis.

关键词： Arabidopsis thaliana HY5 light signal phyB PIFs starch synthesis

The RUBY reporter for visual selection in soybean genome editing

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aBIOTECH 2024年第2期5卷 209-213页

作者： Li Chen Yupeng Cai Xiaoqian Liu Weiwei Yao Shuiqing Wu Wensheng Hou state key laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Agriculture key laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Current systems to screen for transgenic soybeans(Glycine max)involve laborious molecular assays or the expression of fluorescent markers that are difficult to see in soybean ***,a visual system for early screening of transgenic plants would increase the efficiency of crop improvement by genome *** RUBY reporter system,which consists of three genes encoding betalain biosynthetic enzymes,leading to the accumulation of purple pigment in transgenic tissue,has been employed in some plants and dikaryon ***,we assessed the RUBY reporter for visual verification during soybean *** show that RUBY can be expressed in soybean,allowing for visual confirmation of transgenic events without the need for specialized *** with visible accumulation of purple pigment in any tissue were successfully transformed,confirming the accuracy of the RUBY system as a visual *** also assessed the genetic stability of the transgene across generations,which can be performed very early,using the cotyledons of the ***-free seedlings have a distinct green color,facilitating the selection of genome-edited but transgene-free soybean seedlings for *** the RUBY system,we quickly identified a transgene-free Gmwaxy mutant in the T1 *** system thus provides an efficient and convenient tool for soybean genome editing.

关键词： Soybean RUBY Visual reporter Genome editing Biotechnology

Trade-offs between the accumulation of cuticular wax and jasmonic acid-mediated herbivory resistance in maize

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Journal of Integrative Plant Biology 2024年第1期66卷 143-159页

作者： Jiong Liu Lu Li Zhilong Xiong Christelle AMRobert Baozhu Li Shan He Wenjie Chen Jiasheng Bi Guanqing Zhai Siyi Guo Hui Zhang Jieping Li Shutang Zhou Xi Zhang Chun‐Peng Song School of Life Sciences Henan UniversityKaifeng 475004China state key laboratory of crop Stress Adaptation and improvement Henan UniversityKaifeng 475004China state key laboratory of Cotton Bio‐Breeding and Integrated Utilization Henan UniversityKaifeng 475004China Sanya Institute of Henan University Sanya 572025China Institute of Plant Sciences University of BernBern 3013Switzerland

Plants have evolved complex physical and chemical defense systems that allow them to withstand herbivory *** of a complex mixture of very-long-chain fatty acids(VLCFAs)and their derivatives,cuticular wax constitutes the first physical line of defense against ***,we report the function of Glossy 8(ZmGL8),which encodes a 3-ketoacyl reductase belonging to the fatty acid elongase complex,in orchestrating wax production and jasmonic acid(JA)-mediated defenses against herbivores in maize(Zea mays).The mutation of GL8 enhanced chemical defenses by activating the JA-dependent *** observed a trade-off between wax accumulation and JA levels across maize glossy mutants and 24 globally collected maize inbred *** addition,we demonstrated that mutants defective in cuticular wax biosynthesis in Arabidopsis thaliana and maize exhibit enhanced chemical *** transcriptomic and lipidomic analyses indicated that the gl8 mutant confers chemical resistance to herbivores by remodeling VLCFA-related lipid metabolism and subsequent JA biosynthesis and *** results suggest that VLCFA-related lipid metabolism has a critical role in regulating the trade-offs between cuticular wax and JA-mediated chemical defenses.

关键词： cuticular wax fall armyworm herbivore resistance jasmonic acid maize plant-herbivore interactions

Molecular Mechanism of Rice Necrotic Lesion for Optimized Yield and Disease Resistance

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Rice science 2024年第3期31卷 285-299页

作者： HOU Xinyue WANG Yuping QIAN Qian REN Deyong state key laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China state key laboratory of crop Gene Exploration and Utilization in Southwest china Rice Research InstituteSichuan Agricultural UniversityChengdu 611130China

How to balance rice resistance and yield is an important issue in rice *** with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of ***,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance *** review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion ***,we review the molecular regulatory pathways of genes involved in rice disease ***,we summarize the relationship between resistance and yield in rice using newly developed gene editing *** discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

关键词： rice necrotic lesion regulation mechanism high yield high resistance

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences state key laboratory of Rice Biology China National Rice Research Institute National key Facility for crop Gene Resources and Genetic improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

Editing of eIF(iso)4E.c confers resistance against Turnip mosaic virus in Brassica rapa

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Horticultural Plant Journal 2024年第4期10卷 1020-1034页

作者： Yujia Liu Xiaoyun Xin Peirong Li Weihong Wang Yangjun Yu Xiuyun Zhao Deshuang Zhang Jiao Wang Fenglan Zhang Shujiang Zhang Shuancang Yu Tongbing Su state key laboratory of Vegetable Biobreeding Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China National Engineering Research Center for Vegetables Beijing Key Laboratory of Vegetable Germplasms ImprovementKey Laboratory of Biology and Genetics Improvement of Horticultural Crops(North China)Key Laboratory of Urban Agriculture(North)of Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

Turnip mosaic virus(TuMV)constitutes one of the primary diseases affecting Brassica rapa,severely impacting its production and resulting in crop failures in various regions *** research has demonstrated the significance of plant translation initiation factors,specifically the eIF4E and eIF4G family genes,as essential recessive disease resistance *** our study,we conducted evolutionary and gene expression studies,leading us to identify e IF(iso)4E.c as a potential TuMV-resistant *** CRISPR/Cas9 technology,we obtained mutant *** plants with edited eIF(iso)4E.c *** confirmed eIF(iso)4E.c confers resistance against TuMV through phenotypic observations and virus content ***,we employed ribosome profiling assays on eif(iso)4e.c mutant seedlings to unravel the translation landscape in response to ***,we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels(R^(2)=0.729).Comparative analysis of ribosome profiling and RNA-seq data revealed that plant-pathogen interaction,and MAPK signaling pathway-plant pathways were involved in eIF(iso)4E.c-mediated TuMV *** analysis revealed that sequence features,coding sequence length,and normalized minimal free energy,influenced the translation efficiency of *** study highlights that the loss of e IF(iso)4E.c can result in a highly intricate translation mechanism,acting synergistically with transcription to confer resistance against TuMV.

关键词： Brassica rapa eIF(iso)4E.c TuMV Ribo-seq