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Ca^(2+)-independent ZmCPK2 is inhibited by Ca^(2+)-dependent ZmCPK17 during drought response in maize

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Journal of Integrative Plant Biology 2024年第7期66卷 1313-1333页

作者： Xiaoying Hu Jinkui Cheng Minmin Lu Tingting Fang Yujuan Zhu Zhen Li Xiqing Wang Yu Wang Yan Guo Shuhua Yang Zhizhong Gong State key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCenter for Crop Functional Genomics and Molecular BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China College of Life Sciences Institute of Life Science and Green DevelopmentHebei UniversityBaoding 071002China

Calcium oscillations are induced by different ***-dependent protein kinases(CDPKs/CPKs)are one major group of the plant calcium decoders that are involved in various processes including drought *** CPKs are ***,we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize *** found that ZmCPK2 does not bind calcium,and its activity is mainly inhibited during short term abscisic acid(ABA)treatment,and dynamically changed in prolonged ***,ZmCPK2 interacts with and is inhibited by calcium-dependent ZmCPK17,a positive regulator of drought resistance,which is activated by ***17 could prevent the nuclear localization of ZmCPK2 through phosphorylation of ***2 interacts with and phosphorylates and activates ZmYAB15,a negative transcriptional factor for drought *** results suggest that drought stress-induced Ca^(2+)can be decoded directly by ZmCPK17 that inhibits ZmCPK2,thereby promoting plant adaptation to water deficit.

关键词： CDPK drought response phosphorylation stomatal movement transcriptional regulation

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

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

CrisprStitch:Fast evaluation of the efficiency of CRISPR editing systems

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Plant Communications 2024年第3期5卷 13-16页

作者： Yangshuo Han Guanqing Liu Yuechao Wu Yu Bao Yong Zhang Tao Zhang Jiangsu key laboratory of crop Genomics and molecular breeding/Zhongshan Biological breeding laboratory/key laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Jiangsu key laboratory of crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China Chongqing key laboratory of Plant Resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm Creation in Western China(Chongqing)Science CitySchool of Life SciencesSouthwest UniversityChongqing 400715China

Dear Editor,Targeted genome-editing technology using designed nucleases has been rapidly advancing and catalyzing significant breakthroughs in the life ***-designed CRISPR editing experiments can be efficiently evaluated through nextgeneration sequencing(NGS).Nevertheless,NGS data analysis currently lacks a user-friendly pipeline capable of automatically calculating mutations and evaluating editing efficiency in bulk,as well as providing a more comprehensive visualization of results.

关键词： breakthrough editing efficiency

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que key laboratory of Sugarcane Biology and Genetic breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National key laboratory for Tropical crop breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen ***,the resistance mechanisms of WRKY genes in sugarcane remain *** the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense *** identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar *** gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)***,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium ***,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani *** and caused down-regulated expression of immune marker-related *** analysis indicated suppressed expression of most JAZ genes in the signal transduction ***4 interacted with ScJAZ13 to repress its *** thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling *** present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

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

Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize

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molecular Plant 2024年第5期17卷 788-806页

作者： Tao Yang Yunqin Huang Longyu Liao Shanshan Wang Haoyu Zhang Jingying Pan Yongcai Huang Xiaoling Li Di Chen Tao Liu Xiaoduo Lu Yongrui Wu State key laboratory of crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130SichuanChina National key laboratory of Plant molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China Institute of molecular breeding for Maize Qilu Normal UniversityJinanChina

During maize endosperm filling,sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this ***,the molecular mechanisms underlying sucrose and endosperm filling are poorly *** this study,we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2(O2),coordinating with storage-reserve *** showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation,but sucrose can release this *** assays revealed that SnRK1a1 phosphorylates O2 at serine 41(S41),negatively affecting its protein stability and transactivation *** observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves,while overexpression of SnRK1a1 causes the opposite *** of the native O2(O2-OE),phospho-dead(O2-SA),and phospho-mimetic(O2-SD)variants all increased 100-kernel *** O2-SA seeds exhibit smaller kernel size,they have higher accumulation of starch and proteins,resulting in larger vitreous endosperm and increased test weight.O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight.O2-OE seeds show elevated kernel dimensions and nutrient storage,like a mixture of O2-SA and O2-SD ***,our study discovers a novel regulatory mechanism of maize endosperm *** of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.

关键词： maize Opaque2 SnRK1 endosperm phosphorylation sucrose

RETINOBLASTOMA RELATED 1 switches mitosis to meiosis in rice

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Plant Communications 2024年第6期5卷 193-212页

作者： Yongjie Miao Hanli You Huixin Liu Yangzi Zhao Jiangzhe Zhao Yafei Li Yi Shen Ding Tang Baohui Liu Kewei Zhang Zhukuan Cheng Guangdong Provincial key laboratory of Plant Adaptation and molecular Design Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China Jiangsu key laboratory of crop Genomics and molecular breeding/Zhongshan Biological breeding laboratory/key laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China State key laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Zhejiang Provincial key laboratory of Biotechnology on Specialty Economic Plants Department of BiologyCollege of Life SciencesZhejiang Normal UniversityJinhua 321004China Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Jiangsu key laboratory of crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

The transition from mitosis to meiosis is a critical event in the reproductive development of all sexually reproducing ***,the mechanisms that regulate this process in plants remain largely ***,we find that the rice(Oryza sativa L.)protein RETINOBLASTOMA RELATED 1(RBR1)is essential to the transition from mitosis to *** of RBR1 function results in hyper-proliferative sporogenous-celllike cells(SCLs)in the anther locules during early stages of reproductive *** hyperproliferative SCLs are unable to initiate meiosis,eventually stagnating and degrading at late developmental stages to form pollen-free *** results suggest that RBR1 acts as a gatekeeper of entry into ***,cytokinin content is significantly increased in rbr1 mutants,whereas the expression of type-B response factors,particularly LEPTO1,is significantly *** the known close association of cytokinins with cell proliferation,these findings imply that hyper-proliferative germ cells in the anther locules may be attributed to elevated cytokinin concentrations and disruptions in the cytokinin *** a genetic strategy,the association between germ cell hyper-proliferation and disturbed cytokinin signaling in rbr1 has been *** summary,we reveal a unique role of RBR1 in the initiation of meiosis;our results clearly demonstrate that the RBR1 regulatory module is connected to the cytokinin signaling pathway and switches mitosis to meiosis in rice.

关键词： RETINOBLASTOMA RELATED1 meiosis initiation cytokinin rice

Development of Machine Learning Methods for Accurate Prediction of Plant Disease Resistance

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Engineering 2024年第9期40卷 100-110页

作者： Qi Liu Shi-min Zuo Shasha Peng Hao Zhang Ye Peng Wei Li Yehui Xiong Runmao Lin Zhiming Feng Huihui Li Jun Yang Guo-Liang Wang Houxiang Kang State key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Zhongshan Biological breeding laboratory&Jiangsu key laboratory of crop Genomics and molecular breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Hunan Provincial key laboratory of crop Germplasm Innovation and Utilization and College of Agronomy Hunan Agricultural UniversityChangsha 410128China State key laboratory of crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Plant Protection Hunan Agricultural UniversityChangsha 410128China key laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests Ministry of Education College of Plant ProtectionHainan UniversityHaikou 570228China MARA key laboratory of Surveillance and Management for Plant Quarantine Pests Department of Plant BiosecurityCollege of Plant ProtectionChina Agricultural UniversityBeijing 100193China Department of Plant Pathology Ohio State UniversityColumbusOH 43210USA

The traditional method of screening plants for disease resistance phenotype is both time-consuming and *** selection offers a potential solution to improve efficiency,but accurately predicting plant disease resistance remains a *** this study,we evaluated eight different machine learning(ML)methods,including random forest classification(RFC),support vector classifier(SVC),light gradient boosting machine(lightGBM),random forest classification plus kinship(RFC_K),support vector classification plus kinship(SVC_K),light gradient boosting machine plus kinship(lightGBM_K),deep neural network genomic prediction(DNNGP),and densely connected convolutional networks(DenseNet),for predicting plant disease *** results demonstrate that the three plus kinship(K)methods developed in this study achieved high prediction ***,these methods achieved accuracies of up to 95%for rice blast(RB),85%for rice black-streaked dwarf virus(RBSDV),and 85%for rice sheath blight(RSB)when trained and applied to the rice diversity panel I(RDPI).Furthermore,the plus K models performed well in predicting wheat blast(WB)and wheat stripe rust(WSR)diseases,with mean accuracies of up to 90%and 93%,*** assess the generalizability of our models,we applied the trained plus K methods to predict RB disease resistance in an independent population,rice diversity panel II(RDPII).Concurrently,we evaluated the RB resistance of RDPII cultivars using spray *** the predictions with the spray inoculation results,we found that the accuracy of the plus K methods reached 91%.These findings highlight the effectiveness of the plus K methods(RFC_K,SVC_K,and lightGBM_K)in accurately predicting plant disease resistance for RB,RBSDV,RSB,WB,and *** methods developed in this study not only provide valuable strategies for predicting disease resistance,but also pave the way for using machine learning to streamline genome-based crop breeding.

关键词： Predicting plant disease resistance Genomic selection Machine learning Genome-wide association study