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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu Key laboratory of Crop Genetics and Physiology/Key laboratory of plant Functional Genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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molecular plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State Key laboratory of Rice Biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National Key laboratory of plant molecular Genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China Key laboratory of plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State Key laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China Department of molecular Biology and Center for Computational and Integrative Biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

Unveiling a new regulator: Vacuolar V-ATPase mediates brassinosteroid signaling in Arabidopsis

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molecular plant 2024年第2期17卷 227-229页

作者： Shikha Malik Justin W.Walley Department of plant pathology Entomologyand Microbiologylowa State UniversityAmesIA 50011USA

plant growth and development are intricately regulated by hormones such as auxins,gibberellins,jamonates,cytokinins,and brassinosteroids(BRs).BRs are a group of plant steroid hormones that play a vital role in plant growth and response to the *** regulate many biological processes including cell elongation,cell division,and male fertility,as well as abiotic and biotic stress responses.

关键词： media fertility brassinosteroid

PE6c greatly enhances prime editing in transgenic rice plants

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Journal of Integrative plant Biology 2024年第9期66卷 1864-1870页

作者： Zhenghong Cao Wei Sun Dexin Qiao Junya Wang Siyun Li Xiaohan Liu Cuiping Xin Yu Lu Syeda Leeda Gul Xue‐Chen Wang Qi-Jun Chen State Key laboratory of plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing100193China Center for Crop Functional Genomics and molecular Breeding China Agricultural UniversityBeijing 100193China

Prime editing is a versatile CRISPR/Cas-based precise genome-editing technique for crop *** new types of prime editors(PEs)named PE6a–d were recently generated using evolved and engineered reverse transcriptase(RT)variants from three different *** this study,we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double-RT modules in transgenic rice(Oryza sativa)***6c,with an evolved and engineered RT variant from the yeast Tf1 retrotransposon,yielded the highest prime-editing *** average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 *** also demonstrated the feasibility of using two RT modules to improve prime-editing *** results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot *** addition,our findings have laid a foundation for prime-editing-based breeding of rice varieties with enhanced agronomically important traits.

关键词： genome editing PE6 PE6c prime editing prime editor rice

Computational tools for plant genomics and breeding

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Science China(Life Sciences) 2024年第8期67卷 1579-1590页

作者： Hai Wang Mengjiao Chen Xin Wei Rui Xia Dong Pei Xuehui Huang Bin Han State Key laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed laboratory Sanya 572025China State Key laboratory of Tree Genetics and Breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China Shanghai Key laboratory of plant molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Horticulture South China Agricultural UniversityGuangzhou 510640China National Center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200233China

plant genomics and crop breeding are at the intersection of biotechnology and information *** by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome *** advances further revolutionized three directions of *** is genetic dissection of complex traits in crops,along with genomic prediction and *** second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant *** third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic *** three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

关键词： bioinformatics plant genomics breeding by design

The NAC056 transcription factor confers freezing tolerance by positively regulating expression of CBFs and NIA1 in Arabidopsis

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plant Communications 2024年第7期5卷 251-260页

作者： Peipei Xu Wei Ma Huafeng Feng Weiming Cai laboratory of Photosynthesis and Environment CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesNo.300 Fenglin RoadShanghai 200032China State Key laboratory of NBC Protection for Civilian Beijing 102205China Department of Food Science College of Hospitality ManagementShanghai Business SchoolShanghai 200235China These authors contributed equally to this article

Freezing stress can seriously affect plant growth and development,but the mechanisms of these effects and plant responses to freezing stress require further ***,we identified a NAM,ATAF1/2,and CUC2(NAC)-family transcription factor(TF),NAC056,that can promote freezing tolerance in ***056 mRNA levels are strongly induced by freezing stress in roots,and the nac056 mutant exhibits compromised freezing ***056 acts positively in response to freezing by directly promoting key C-repeat-binding factor(CBF)pathway ***,we found that CBF1 regulates nitrate assimilation by regulating the nitrate reductase gene NIA1 in plants;therefore,NAC056–CBF1–NIA1 form a regulatory module for the assimilation of nitrate and the growth of roots under freezing *** addition,35S::NAC056 transgenic plants show enhanced freezing tolerance,which is partially reversed in the cbfs triple ***,NAC056 confers freezing tolerance through the CBF pathway,mediating plant responses to balance growth and freezing stress tolerance.

关键词： CBFs freezing tolerance NAC transcription factor nitrate assimilation root growth

Developing guanine base editors for G-to-T editing in rice

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Journal of Integrative plant Biology 2024年第8期66卷 1557-1560页

作者： Lang Liu Zhongming Zhang Chenyang Wang Fang Yan Wenxian Sun Xueping Zhou Weiguo Miao Huanbin Zhou State Key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Department of plant pathology China Agricultural UniversityBeijing 100193China Scientiﬁc Observing and Experimental Station of Crop Pests in Guilin Ministry of Agriculture and Rural AffairsGuilin 541399China School of plant Protection Hainan UniversityHaikou 570228China State Key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Key laboratory of Gene Editing Technologies Ministry of Agricultural and Rural AffairsSanya 572024China

Single nucleotide polymorphisms (SNPs) are widely present and related to desirable agronomic traits in *** regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated base editors have been frequently used to correct defective alleles and create novel alleles by artificial evolution for rapid crop genetic improvement (Ma et al.,2021).

关键词： alleles agronomic base

Decoding the biochemical dialogue:metabolomic insights into soybean defense strategies against diverse pathogens

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Science China(Life Sciences) 2024年第10期67卷 2234-2250页

作者： Min Qiu Mengjun Tian Yaru Sun Huaibo Li Wenwen Huang Haibing Ouyang Shaoyan Lin Chen Zhang Ming Wang Yuanchao Wang Sanya Institute of Nanjing Agricultural University Department of Plant PathologyNanjing Agricultural UniversityNanjing 210095China The Key laboratory of plant Immunity Nanjing Agricultural UniversityNanjing 210095China Key laboratory of Soybean Disease and Pest Control(Ministry of Agriculture and Rural Affairs) Nanjing Agricultural UniversityNanjing 210095China China State Key laboratory of Crop Genetics&Germplasm Enhancement and Utilization Nanjing Agricultural UniversityNanjing 210095China

Soybean,a crucial global leguminous crop,confronts persistent threats from diverse pathogens,exerting a profound impact on global *** genetic dimensions of soybean-pathogen interactions have garnered attention,the intricate biochemical responses remain poorly *** this study,we applied targeted and untargeted liquid chromatography coupled to mass spectrometry(LC-MS)metabolite profiling to dissect the complex interplay between soybeans and five distinct *** analysis uncovered 627 idMS/MS spectra,leading to the identification of four main modules,encompassing flavonoids,isoflavonoids,triterpenoids,and amino acids and peptides,alongside other compounds such as *** shifts were observed in both primary and secondary metabolism in response to pathogenic *** notable were the bidirectional changes in total flavonoids across diverse pathogenic inoculations,while triterpenoids exhibited a general declining *** among the highly inducible total flavonoids were known representative antipathogen compounds(glyceollin I),backbone forms of isoflavonoids(daidzein,genistein,glycitein,formononetin),and newly purified compounds in this study(prunin).Subsequently,we delved into the biological roles of these five compounds,validating their diverse functions against pathogens:prunin significantly inhibited the vegetative growth and virulence of Phytophthora sojae;genistein exhibited a pronounced inhibitory effect on the vegetative growth and virulence of Phomopsis longicolla;daidzein and formononetin displayed significant repressive effects on the virulence of *** study underscores the potent utility of metabolomic tools,providing in-depth insights into plant-pathogen interactions from a biochemical *** findings not only contribute to plant pathology but also offer strategic pathways for bolstering plant resistance against diseases on a broader scale.

关键词： metabolome soybean soybean-pathogens interaction secondary metabolites triterpenoids flavonoids isoflavonoids antimicrobial compounds

A glycine-rich nuclear effector VdCE51 of Verticillium dahliae suppresses plant immune responses by inhibiting the accumulation of GhTRXH2

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The Crop Journal 2024年第4期12卷 1137-1149页

作者： Chi Li Yingqi Huang Wenjing Shang Jieyin Chen Steven J.Klosterman Krishna V.Subbarao Jun Qin Xiaoping Hu State Key laboratory of Crop Stress Resistance and High-Efficiency Production Key Laboratory of Plant Protection Resources and Pest Management of Ministry of EducationKey Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural AffairsCollege of Plant ProtectionNorthwest A&F UniversityYangling 712100ShaanxiChina State Key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Western Agricultural Research Center Chinese Academy of Agricultural SciencesChangji 831100XinjiangChina Agricultural Research Service United States Department of AgricultureSalinasCA 93905USA Department of plant pathology University of CaliforniaDavisc/o United States Agricultural Research StationSalinasCA 93905USA

Verticillium dahliae is an important soil-borne fungal pathogen that causes great yield losses in many cash *** of this fungus are known to regulate plant immunity but the mechanism much remains unclear.A glycine-rich nuclear effector,VdCE51,was able to suppress immune responses in tobacco against Botrytis cinerea and Sclerotinia *** effector was a required factor for full virulence of ***,and its nuclear localization was a requisite for suppressing plant *** thioredoxin GhTRXH2,identified as a positive regulator of plant immunity,was a host target of *** findings show a virulence regulating mechanism whereby the secreted nuclear effector VdCE51 interferes with the transcription of PR genes,and the SA signaling pathway by inhibiting the accumulation of GhTRXH2,thus suppressing plant immunity.

关键词： Verticillium dahliae plant immunity Effector Thioredoxin