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Transcriptome-wide profiling of RNA N^(4)-cytidine acetylation in Arabidopsis thaliana and Oryza sativa

Molecular Plant 2023年第6期16卷 1082-1098页

作者： Bin Li Donghao Li Linjun Cai Qiting Zhou Cong Liu Jianzhong Lin Yixing Li Xiaoying Zhao Li Li Xuanming Liu Chongsheng He College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan Engineering and Technology Research Center of Hybrid RapeseedHunan UniversityChangsha410082 Hunan 410082China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina

Acetylation of N^(4)-cytidine(ac^(4)C)has recently been discovered as a novel modification of mRNA.RNA ac^(4)C modification has been shown to be a key regulator of RNA stability,RNA translation,and the thermal stress response.However,its existence in eukaryotic mRNAs is still controversial.In plants,the existence,distribution pattern,and potential function of RNA ac^(4)C modification are largely unknown.Here we report the presence of ac^(4)C in the mRNAs of both Arabidopsis thaliana and rice(Oryza sativa).By comparing two ac^(4)C sequencing methods,we found that RNA immunoprecipitation and sequencing(acRIP-seq),but not ac^(4)C sequencing,was suitable for plant RNA ac^(4)C sequencing.We present transcriptome-wide atlases of RNA ac^(4)C modification in A.thaliana and rice mRNAs obtained by acRIP-seq.Analysis of the distribution of RNA ac^(4)C modifications showed that ac^(4)C is enriched near translation start sites in rice mRNAs and near translation start sites and translation end sites in Arabidopsis mRNAs.The RNA ac^(4)C modification level is positively correlated with RNA half-life and the number of splicing variants.Similar to that in mammals,the translation efficiency of ac^(4)C target genes is significantly higher than that of other genes.Our in vitro translation results confirmed that RNA ac^(4)C modification enhances translation efficiency.We also found that RNA ac^(4)C modification is negatively correlated with RNA structure.These results suggest that ac^(4)C is a conserved mRNA modification in plants that contributes to RNA stability,splicing,translation,and secondary structure formation.

关键词： N^(4)-acetylcytidine epitranscriptome Arabidopsis thaliana Oryza sativa

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Identification and cell wall analysis of interspecific hybrids between Oryza sativa and oryza ridleyi

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Journal of Integrative Agriculture 2017年第8期16卷 1676-1681页

作者： YI Chuan-deng LI Wei WANG De-rong JIANG Wei HU Da-bang ZHOU Yong LIANG Guo-hua GUMing-hong Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of Ministry of EducationYangzhou UniversityYangzhou 225009P.R.China

oryza ridleyi is an allotetraploid wild species with the HHJJ genome, and Oryza sativa is a diploid cultivated rice that has the AA genome. Although the wide hybrid between the two species is difficult to obtain, we overcome this difficulty by young embryo rescue. An obvious heterosis was primarily found for the plant height, tillering ability, vegetative vigor, etc. However, the hybrid panicle and culm traits were found to resemble that of the wild rice parent, O. ridleyi, for the long awns, exoteric purple stigma, grain shattering, dispersed panicles, and culm mechanical strength. Genomic in situ hybridization （GISH） analysis was subsequently performed on the mitotic metaphase chromosome of the root tips, and we determined that the hybrid is an allotriploid with 36 chromosomes and its genomic constitution is AHJ. Chemical analyses conducted on the culm of O. sativa, O. ridleyi, and their interspecific hybrids showed that major changes occurred in the xylose, glucose, and arabinose concentrations, which are correlated with the specific hemicellulose polymer and cellulose components that are important in the primary cell walls of green plants. Meanwhile, the culm anatomical analyses indicated that additional large vascular bundles and an extra sclerenchyma cell layer were found in O. ridleyi. Additionally, further thickening of the secondary cell walls of the cortical fiber sclerenchyma cells and the phloem companion cells was discovered in O. ridleyi and in the interspecific hybrids. These results imply that there may be a potential link between culm mechanical strength and culm anatomical structure.

关键词： Oryza sativa oryza ridleyi interspecific hybrid genomic in situ hybridization cell wall

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Overexpression of OsKTN80a, a katanin P80ortholog, caused the repressed cell elongation and stalled cell division mediated by microtubule apparatus defects in primary root in Oryza sativa

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Journal of Integrative Plant Biology 2014年第7期56卷 622-634页

作者： Lei Wan Xiuwen Wang Shaoqing Li Jun Hu Wenchao Huang Yingguo Zhu State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University

Katanin, a microtubule-severing enzyme, consists of two subunits：the catalytic subunit P60, and the regulatory subunit P80. In several species, P80 functions in meiotic spindle organization, the flagella biogenesis, the neuronal development, and the male gamete production. However, the P80 function in higher plants remains elusive. In this study, we found that there are three katanin P80 orthologs （OsKTN80a, OsKTN80b, and OsKTN80c） in Oryza sativa L. Overexpression of OsKTN80a caused the retarded root growth of rice seedlings. Further investigation indicates that the retained root growth was caused by the repressed cell elongation in the elongation zone and the stalled cytokinesis in the division zone in the root tip. The in vivo examination suggests that OsKTN80a acts as a microtubule stabilizer. We＆amp;nbsp;prove that OsKTN80a, possibly associated with OsKTN60, is involved in root growth via regulating the cell elongation and division.

关键词： Cell division cell expansion Oryza sativa OsKTN8oa rootgrowth

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Developing herbicide resistant Sri-lankan rice(Oryza sativa L.)varieties:An application of Self Organizing Map

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Information Processing in Agriculture 2017年第2期4卷 140-149页

作者： E.M.S.I.Ekanayaka S.R.Weerakoon S.Somaratne O.V.D.S.J.Weerasena Department of Botany The Open University of Sri LankaP.O.Box 21NawalaSri Lanka Institutes of Biochemistry Molecular Biology and BiotechnologyUniversity of ColomboSri Lanka

Application of high concentrations of post-emergent broad spectrum systemic herbicide,glyphosate is prevalently used to control rice weeds in Asian countries including Sri Lanka.Off target movements of glyphosate adversely affect growth of the rice plant reducing the yield.Inducing herbicide resistance(HR)in cultivated rice is a novel approach to enhance selectivity and crop safety.Studies on induced HR in Sri Lankan rice varieties are limited and studies are required to include HR rice in a cropping program.Ethyl Methyl Sulfonate(EMS),a chemical mutagen is used for functional mutations.The present study is an attempt of raising HR rice lines through conventional breeding methods.A suitable glyphosate concentration was determined by a preliminary study using five rice varieties(Bg300,Bg352,At362,Bg379-2 and H4)and varying glyphosate concentrations(0.25 g/l,0.5 g/l,1 g/l,2 g/l and 3 g/l).Resistance percentage50%was arbitrary considered as resistant varieties.Complete Randomized Design with three replicates was used in the experiment.Agromorphological characters were recorded for the survived plants.Twelve varieties(Bg359,At362,Bw364,Ld365,Bg366,Bg369,Bg379-2,Bg403,Bg454“Pachcha perumal”,“Kalu heenati”and“Kurulu thuda”)showed natural resistance to glyphosate and fourteen varieties have increased resistance after mutagenesis by EMS(S0-First generation).HR resistance percentage of S1(Second generation)plants was similar to S0 plants indicating HR was transferred to new generation.Conventional statistics was supplemented with Self-Organizing Maps(SOM)to visualize variation of agro-morphological characters under treatment.The result proved that EMS application is an effective method in breeding new rice germplasm with HR and SOM is an important tool for visualizing the multi-dimensional dataset in lower dimensions.

关键词： Ethyl Methyl Sulfonate Glyphosate Herbicide resistance Oryza sativa Self-Organizing Map

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Crossability Barriers in the Interspecific Hybridization between Oryza sativa and O.meyeriana

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Journal of Integrative Plant Biology 2009年第1期51卷 21-28页

作者： Xue-Lin Fu Yong-Gen Lu Xiang-Dong Liu Jin-Quan Li Guangdong Provincial Key Laboratory of Plant Molecular Breeding South China Agricultural University Guangzhou 510642 China

oryza meyeriana Baill （GG genome） is a precious germplasm in the tertiary gene pool of cultivated rice （AA genome）, and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspeciflc crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons underlying incrossability were investigated in the present report. The results showed that：（i） at 3-7 d after pollination （DAP）, many hybrid embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form at 3 DAP, leading to nutrition starvation for young embryo development; （ii） at 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability barriers in the interspecific hybridization between O. sativa and O. meyeriana are discussed.

关键词： crossability embryo development interspecific hybridization Oryza sativa O. meyeriana.

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DDG1 and G Protein α Subunit RGA1 Interaction Regulates Plant Height and Senescence in Rice(Oryza sativa)

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Phyton-International Journal of Experimental Botany 2023年第7期92卷 2051-2064页

作者： Xi Liu Chuxuan Zhao Di Wang Gen Pan Xiaonan Ji Su Gao Tanxiao Du Yating Feng Wenjing Chen Jiangsu Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake Regional Cooperative Innovation Center for Modern Agriculture and Environmental ProtectionHuaiyin Normal UniversityHuai’an223300China School of Life Sciences Huaiyin Normal UniversityHuai’an223300China Crop Research and Development Center Huaiyin Institute of Agricultural Sciences of Xuhuai Region in JiangsuHuai’an223001China Institute of Bast Fiber Crops Chinese Academy of Agricultural SciencesChangsha410205China

Many studies have already shown that dwarfism and moderate delayed leaf senescence positively impact rice yield,but the underlying molecular mechanism of dwarfism and leaf senescence remains largely unknown.Here,using map-based cloning,we identified an allele of DEP2,DDG1,which controls plant height and leaf senescence in rice.The ddg1 mutant displayed dwarfism,short panicles,and delayed leaf senescence.Compared with the wild-type,ddg1 was insensitive to exogenous gibberellins(GA)and brassinolide(BR).DDG1 is expressed in various organs,especially in stems and panicles.Yeast two-hybrid assay,bimolecular fluorescent complementation and luciferase complementation image assay showed that DDG1 interacts with theα-subunit of the heterotrimeric G protein.Disruption of RGA1 resulted in dwarfism,short panicles,and darker-green leaves.Furthermore,we found that ddg1 and the RGA1 mutant was more sensitive to salt treatment,suggesting that DDG1 and RGA1 are involved in regulating salt stress response in rice.Our results show that DDG1/DEP2 regulates plant height and leaf senescence through interacting with RGA1.

关键词： Oryza sativa DDG1 plant height senescence RGA1

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The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice

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Molecular Plant 2008年第5期1卷 839-850页

作者： Chuanzhu Fana Yong Zhang Yeisoo Yu Steve Rounsley Manyuan Long Rod A. Wing Arizona Genomics Institute Department of Plant Sciences University of Arizona Tucson AZ 85721 USA Department of Ecology and Evolution University of Chicago Chicago IL 60637 USA BIO5 Institute for Collaborative Research University of Arizona Tucson AZ 85721 USA

Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago （MYA）. For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.

关键词： comparative genomics gene duplication Oryza sativa subtelomere new genes.

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Vlodulation of ABA Signaling by Altering VxGФL Vlotif of PP2Cs in Oryza sativa

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Molecular Plant 2017年第9期10卷 1190-1205页

作者： Seungsu Han

The abscisic acid （ABA） signaling pathway is regulated by clade A type 2C protein phosphatases （PP2CAs） in plants. In the presence of ABA, PP2Cs release stress/ABA-activated protein kinases by binding to ABA-bound receptors （PYL/RCARs） for activation. Although the wedging tryptophan in PP2Cs is critical in the interaction with PYL/RCARs in Arabidopsis and rice, it remains elusive as to how other interface regions are involved in the interaction. Here, we report the identification of a conserved region on PP2Cs, termed the VxG4ФL motif, which modulates the interaction with PYL/RCARs through its second and fourth residues. The effects of the second and fourth residues on the interaction of OsPP2CS0 with several OsPYIJRCAR proteins were investigated by systematic mutagenesis. One OsPP2C50 mutant, VFGML （＂FM＂） mutant, lowered the affinity to OsPYL/RCAR3 by Ф15-fold in comparison with the wUd-type. Compar- ison of the crystal structures of wild-type OsPP2C50：ABA：OsPYI./RCAR3 with those composed of FM mutant revealed local conformational changes near the VxGФL motif, further supported by hydrogen-deute- rium exchange mass spectrometry. In rice protoplasts, ABA signaling was altered by mutations in the VxGФL motif. Transgenic Arabidopsis plants overexpressing OsPP2C50 and OsPP2C5OFM showed altered ABA sensitivity. Taken together, the VxGФL motif of PP2Cs appears to modulate the affinity of PP2Cs with PYL/RCARs and thus likely to alter the ABA signaling, leading to the differential sensitivity to ABA in planta.

关键词： ABA receptor type 2C protein phosphatase VxGФL motif Oryza sativa

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Prediction and Expression Analysis of miRNAs Associated with Heat Stress in Oryza sativa

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Rice science 2014年第1期21卷 3-12页

作者： B.SAILAJA S.R.VOLETI D.SUBRAHMANYAM N.SARLA V.VISHNU PRASANTH V.P.BHADANA S.K.MANGRAUTHIA Biotechnology Section Directorate of Rice Research Rajendranagar

Computational prediction of potential microRNAs （miRNAs） and their target genes was performed to identify the miRNAs and genes associated with temperature response in rice. The data of temperature-responsive miRNAs of Arabidopsis, and miRNAs and the whole genome data of rice were used to predict potential miRNAs in Oryza sativa involved in temperature response. A total of 55 miRNAs were common in both the species, and 27 miRNAs were predicted at the first time in rice. Target genes were searched for these 27 miRNAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRNAs showed that majority of the miRNAs were down regulated under heat stress for rice cultivar Nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRNAs during heat stress will advance the understanding of gene regulation under stress in rice.

关键词： miRNA Oryza sativa Arabidopsis target mRNA regulation

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Development and Identification of Introgression Lines from Cross of Oryza sativa and oryza minuta

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Rice science 2013年第2期20卷 95-102页

作者： GUO Si-bin WEI Yu LI Xiao-qiong LIU Kai-qiang HUANG Feng-kuan CHEN Cai-hong GAO Guo-qing Rice Research Institute Guangxi Academy of Agricultural Sciences Guangxi Crop Genetic Improvement and Biotechnology Laboratory Plant Protection Research Institute Guangxi Academy of Agricultural Sciences

Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines（ILs）,which derived from an accession of oryza minuta（accession No.101133） with BBCC genome,as the donor,and an elite indica cultivar IR24（O.sativa）,as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat（SSR） markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64% of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5% 25.2%,with an average of 8.3%.Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.

关键词： Oryza sativa oryza minuta introgression line bacterial blight brown planthopper whitebacked planthopper

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