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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

Effect of inorganic arsenic in paddy soil on the migration and transformation of selenium species in rice plants

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Journal of Environmental Sciences 2024年第9期143卷 35-46页

作者： Ganga Raj Pokhrel Kaiteng Wang Kaiyang Ying Yongchen Wu Ze Wang Xi Zhu Can Qu Hong Li Fengfu Fu Guidi Yang Fujian Provincial Key laboratory of Agroecological Processing and Safety Monitoring Key Laboratory for Medicinal Plant Chemistry and Chemical BiologyCollege of JunCao Science and EcologyFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Chemistry Birendra Multiple CampusTribhuvan UniversityChitwan 00977-44200BharatpurNepal Key laboratory for Analytical Science of Food Safety and Biology of Ministry of Education Fujian Provincial Key Lab of Analysis and Detection for Food SafetyCollege of ChemistryFuzhou UniversityFuzhou 350116China

Selenium(Se)in paddy rice is one of the significant sources of human Se ***,the effect of arsenic(As)pollution in soil on the translocation of Se species in rice plants is *** this research,a pot experiment was designed to examine the effect of the addition of 50 mg As/kg soil as arsenite or arsenate on the migration of Se species from soil to indica Minghui 63 and *** results showed that the antagonism between inorganic As and Se was closely related to the rice cultivar and Se oxidation state in *** to the standalone selenate treatment,arsenite significantly(p<0.05)decreased the accumulation of selenocystine,selenomethionine and selenate in the roots,stems,sheaths,leaves,brans and kernels of both cultivars by 21.4%-100.0%,40.0%-100.0%,41.0%-100%,5.4%-96.3%,11.3%-100.0% and 26.2%-39.7% respectively,except for selenocystine in the kernels of indica Minghui 63 and selenomethionine in the leaves of indica Minghui 63 and the stems of indica *** also decreased(p<0.05)the accumulation of selenocystine,selenomethionine and selenate in the roots,stems,brans and kernels of both cultivars by 34.9%-100.0%,30.2%-100.0%,11.3%-100.0% and 5.6%-39.6%respectively,except for selenate in the stems of indica Minghui ***,relative to the standalone selenite treatment,arsenite and arsenate decreased(p<0.05)the accumulation of selenocystine,selenomethionine and selenite only in the roots of indica Minghui 63 by 45.5%-100.0%.Our results suggested that arsenite and arsenate had better antagonism toward Se species in selenate-added soil than that in selenite-added soil;moreover,arsenite had a higher inhibiting effect on the accumulation of Se species than arsenate.

关键词： Rice(Oryza sativa L.) Inorganic arsenic Selenium species Translocation Antagonistic effect

Sensitivity and resistance risk analysis of Didymella bryoniae populations to fluopyram

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Journal of Integrative Agriculture 2024年第7期23卷 2306-2317页

作者： Zhiwen Wu Xiaowei Cai Xuewei Mao Mingguo Zhou Yiping Hou College of plant Protection Nanjing Agricultural UniversityNanjing 210095China

Fluopyram is an succinate dehydrogenase inhibitors(SDHI)fungicide that has been registered in China to control gummy stem blight(GSB)in watermelons for many ***,whether the field pathogens of GSB are still sensitive to fluopyram or not is ***,we collected 69 Didymella bryoniae isolates from the fields that usually use fluopyram to control GSB to determine the sensitivity *** EC_(50)(50%inhibition effect)values of fluopyram against *** ranged from 0.0691 to 0.3503μg mL^(–1) and the variation factor was *** mean EC_(50) value was(0.1579±0.0669)μg mL^(–1) and the curve of sensitivity was *** resistant strains were found in the isolates,which means that the pathogens were still sensitive to *** minimal inhibition concentration(MIC)of fluopyram against *** was 3μg mL^(–1).Four low-resistant mutants and two medium-resistant mutants were obtained using fungicide taming and the resistance of mutants could be inherited *** growth rate of mutants decreased significantly compared with that of wild-type strains while the biomass of most mutants was similar to that of wild-type *** sensitivity of most resistant mutants to various stresses was increased compared with that of wild-type *** virulence of mutants receded except for low-resistant mutant XN51FR-1,which had the same lesion area as XN51 on the watermelon *** results indicated that the fitness of resistant mutants was decreased compared with that of wild-type *** cross-resistance assay indicated that fluopyram-resistant mutants were positive cross-resistant to all six SDHI fungicides in this test but were still sensitive to fluazinam and *** the resistance risk of *** to fluopyram was *** addition,we found that the SdhB gene of low-resistant mutant XN30FR-1 had three new point mutations at positions K258N,A259P,and ***-resistant mutant XN52FR-1 showed a mutation at position H277N an

关键词： fluopyram D.bryoniae sensitivity risk assessment

Camellia sinensis CsMYB4a participates in regulation of stamen growth by interaction with auxin signaling transduction repressor CsAUX/IAA4

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The Crop Journal 2024年第1期12卷 188-201页

作者： Guoliang Ma Mingzhuo Li Yingling Wu Changjuan Jiang Yifan Chen Dawei Xing Yue Zhao Yajun Liu Xiaolan Jiang Tao Xia Liping Gao School of Life Science Anhui Agricultural UniversityHefei 230036AnhuiChina plant for Human Health Institute Department of Plant and Microbial BiologyNorth Carolina State UniversityKannapolisNC 28081USA State Key laboratory of Tea plant Biology and Utilization/Key laboratory of Tea Biology and Tea Processing of Ministry of Agriculture/Anhui Provincial laboratory of Tea plant Biology and Utilization Anhui Agricultural UniversityHefei 230036AnhuiChina

Subgroup 4(Sg4)members of the R2R3-MYB are generally known as negative regulators of the phenylpropanoid pathway in *** previous research showed that a R2R3-MYB Sg4 member from Camellia sinensis(CsMYB4a)inhibits expression of some genes in the phenylpropanoid pathway,but its physiological function in the tea plant remained ***,CsMYB4a was found to be highly expressed in anther and filaments,and participated in regulating filament *** analysis and exogenous auxin treatment showed that the target of CsMYB4a might be the auxin signal ***/indole-3-acetic acid 4(AUX/IAA4),a repressor in auxin signal transduction,was detected from a yeast two-hybrid screen using CsMYB4a as *** silencing assays showed that both CsIAA4 and CsMYB4a regulate filament *** plants overexpressing CsIAA4 were insensitive to exogenous a-NAA,consistent with overexpression of ***-protein interaction experiments revealed that CsMYB4a interacts with N-terminal of CsIAA4 to prevent CsIAA4 *** out of the endogenous NtIAA4 gene,a CsIAA4 homolog,in tobacco alleviated filament growth inhibition and a-NAA insensitivity in plants overexpressing *** results strongly suggest that CsMYB4a works synergistically with CsIAA4 and participates in regulation of the auxin pathway in stamen.

关键词： AUX/IAA4 Auxin signaling CsMYB4a Subgroup 4 R2R3-MYB

Temporal control of the Aux/IAA genes BnIAA32 and BnIAA34 mediates Brassica napus dual shade responses

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Journal of Integrative plant Biology 2024年第5期66卷 928-942页

作者： Yafei Li Yiyi Guo Yue Cao Pengguo Xia Dongqing Xu Ning Sun Lixi Jiang Jie Dong Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Key laboratory of plant Secondary Metabolism and Regulation of Zhejiang Province College of Life Sciences and MedicineZhejiang Sci-TechUniversityHangzhou310018China State Key laboratory of Crop Genetics and Germplasm Enhancement College of AgricultureNanjing Agricultural UniversityNanjing 210095China Key laboratory of growth Regulation and Transformation Research of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China

Precise responses to changes in light quality are crucial for plant growth and *** example,hypocotyls of shade-avoiding plants typically elongate under shade *** this typical shade-avoidance response(TSR)has been studied in Arabidopsis(Arabidopsis thaliana),the molecular mechanisms underlying shade tolerance are poorly *** we report that ***(Brassica napus)seedlings exhibit dual shade *** addition to the TSR,*** seedlings also display an atypical shade response(ASR),with shorter hypocotyls upon perception of early-shade ***-wide selective sweep analysis indicated that ASR is associated with light and auxin ***,genetic studies demonstrated that phytochrome A(BnphyA)promotes ASR,whereas BnphyB inhibits *** ASR,YUCCA8 expression is activated by early-shade cues,leading to increased auxin *** inhibits hypocotyl elongation,as young *** seedlings are highly sensitive to ***,two non-canonical AUXIN/INDOLE-3-ACETIC ACID(Aux/IAA)repressor genes,BnIAA32 and BnIAA34,are expressed during this early ***32 and BnIAA34 inhibit hypocotyl elongation under shade conditions,and mutations in BnIAA32 and BnIAA34 suppress ***,our study demonstrates that the temporal expression of BnIAA32 and BnIAA34 determines the behavior of *** seedlings following shade-induced auxin biosynthesis.

关键词： Brassica napus high-density planting IAA32/34 light signal transduction shade response temporal gene expression

OsNPF3.1,a nitrate,abscisic acid and gibberellin transporter gene,is essential for rice tillering and nitrogen utilization efficiency

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Journal of Integrative Agriculture 2024年第4期23卷 1087-1104页

作者： Junnan Hang Bowen Wu Diyang Qiu Guo Yang Zhongming Fang Mingyong Zhang Institute of Rice Industry Technology Research/Key laboratory of Functional Agriculture Guizhou Provincial Department of Education/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous RegionMinistry of Education/Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/College of Agricultural SciencesGuizhou UniversityGuiyang 550025China Key laboratory of South China Agricultural plant Molecular analysis and Genetic Improvement/Guangdong Provincial Key laboratory of Applied Botany/South China Botanical Garden Chinese Academy of SciencesGuangzhou 510650China Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesGuangzhou 510640China

Low-affinity nitrate transporter genes have been identified in subfamilies 4-8 of the rice nitrate transporter 1(NRT1)/peptide transporter family(NPF),but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains *** this study,we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency(NUtE).OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars,and its expression is positively associated with tiller *** expression was higher in the basal part,culm,and leaf blade than in other parts of the plant,and was strongly induced by nitrate,abscisic acid(ABA)and gibberellin 3(GA_3)in the root and shoot of *** experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter,with rice protoplast uptake assays showing it to be an ABA and GA_3 ***3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering,especially at high nitrate *** NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations,whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats(CRISPR)plants was increased under high nitrate *** results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate *** altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations,respectively.

关键词： rice tillering grain yield phytohormone nitrate transporter nitrogen utilization efficiency

A circular single-stranded DNA mycovirus infects plants and confers broad-spectrum fungal resistance

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Molecular plant 2024年第6期17卷 955-971页

作者： Xianhong Wang Ioly Kotta-Loizou Robert H.A.Coutts Huifang Deng Zhenhao Han Ni Hong Karim Shafik Liping Wang Yashuang Guo Mengmeng Yang Wenxing Xu Guoping Wang National Key laboratory for Germplasm Innovation&Utilization of Horticultural Crops Wuhan 430070China Hubei Hongshan laboratory Wuhan 430070China College of plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Key lab of plant Pathology of Hubei Province Wuhan 430070China Department of Life Sciences Faculty of Natural SciencesImperial College LondonLondon SW72AZUK Department of Clinical Pharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfield AL109ABUK Department of plant Pathology Faculty of AgricultureAlexandria UniversityAlexandria 21526Egypt

Circular single-stranded DNA(ssDNA)viruses have been rarely found in fungi,and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain *** this study,a novel circular ssDNA virus,tentatively named Diaporthe sojae circular DNA virus 1(DsCDV1),was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear ***1 has a monopartite genome(3185 nt in size)encapsidated in isometric virions(21-26 nm in diameter).The genome comprises seven putative open reading frames encoding a discrete replicase(Rep)split by an intergenic region,a putative capsid protein(CP),several proteins of unknown function(P1-P4),and a long intergenic ***,the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae,respectively,indicating an evolutionary linkage with both *** analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster,supporting the establishment of a new family,tentatively named Gegemycoviridae,intermediate to both ***1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host ***,DsCDV1 can systematically infect tobacco and pear seedlings,providing broad-spectrum resistance to fungal *** localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata,while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus,suggesting that P3 is a movement ***1 exhibits unique molecular and biological traits not observed in other ssDNA viruses,serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and *** findings contribute to expanding our understanding of ssDNA virus diversity and evolution,offering potential biocontrol applications for managing crucial plant d

关键词： circular single-stranded DNA virus mycovirus virus evolution Genomoviridae Gegemycoviridae Diaporthe sojae circular DNA virus 1

A growth-regulating factor 7(GRF7)-mediated gene regulatory network promotes leaf growth and expansion in sugarcane

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The Crop Journal 2024年第2期12卷 422-431页

作者： Qiaoyu Wang Yihan Li Dadong Lin Xiaoxi Feng Yongjun Wang Tianyou Wang Hongyan Ding Jisen Zhang State Key lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key lab for Saccharum Biology Guangxi UniversityNanning 530005GuangxiChina Center for Genomics and Biotechnology/Fujian Provincial Key laboratory of Haixia Applied plant Systems Biology/Key laboratory of Saccharum Biology and Genetic Breeding/National Engineering Research Center for Saccharum Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina

Knowledge of the function of growth-regulating factors(GRFs)in sugarcane(Saccharum officinarum and ***)growth and development could assist breeders in selecting desirable plant ***,limited information about GRFs is available in Saccharum due to their *** this study,22 GRFs were identified in the two species and their conserved domains,gene structures,chromosome location,and synteny were ***7 expression varied among tissues and responded to diurnal ***7-YFP was localized preferentially in the nucleus and appears to act as a transcriptional ***7 positively regulated the size and length of rice leaves,possibly by regulating cell size and plant *** seven potential transcription factors binding to the SsGRF7 promoter in ***,four showed positive expression patterns,and two showed negative expression patterns relative to SsGRF7.

关键词： Expression analysis growth-regulating factor Leaf development Sugarcane Transcription factors

Gibberellin promotes cambium reestablishment during secondary vascular tissue regeneration after girdling in an auxin-dependent manner in Populus

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Journal of Integrative plant Biology 2024年第1期66卷 86-102页

作者： Yufei Zhang Lingyan Wang Yuexin Wu Donghui Wang Xin‐Qiang He State Key laboratory of Protein and plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

Secondary vascular tissue(SVT)development and regeneration are regulated by *** this study,we used an in vitro SVT regeneration system to demonstrate that gibberellin(GA)treatment significantly promotes auxin-induced cambium *** GA content by overexpressing or knocking down ent-kaurene synthase(KS)affected secondary growth and SVT regeneration in *** poplar DELLA gene GIBBERELLIC ACID INSENSITIVE(PtoGAI)is expressed in a specific pattern during secondary growth and cambium regeneration after *** of PtoGAI disrupted poplar growth and inhibited cambium regeneration,and the inhibition of cambium regeneration could be partially restored by GA *** analysis of the PtaDR5:GUS transgenic plants,the localization of PIN-FORMED 1(PIN1)and the expression of auxin-related genes found that an additional GA treatment could enhance the auxin response as well as the expression of PIN1,which mediates auxin transport during SVT *** together,these findings suggest that GA promotes cambium regeneration by stimulating auxin signal transduction.

关键词： auxin cambium gibberellin Populus secondary vascular tissue regeneration