Project description:Rice transitory yellow (RTYV) is the causal agent of rice transitory yellow disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection. Overall design: Comparison between RTYV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons
Project description:Japonica rice cultivar Nipponbare was inoculated with wheat leaf rust (Puccinia triticina f. sp. tritici, non-host pathogen to rice) to compare gene expression profiles with mock-inoculated controls. Although eventually failed in invasion, leaf rust induced a set of rice genes that were distinctally up-regulated, some of those were confirmed by quantitative real-time PCR assays. Overall design: Rice leaves were heavily inoculated with a non-host pathogen, wheat leaf rust fungus, and compared with mock inoculation with 3 biological replications.
Project description:We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq. Overall design: Three-condition experiment, non-treatment vs. phosphate starvation/sufficient treatment of rice seedling. Biological replicates: 3 non-treatment replicates, 3 phosphate starvation/sufficient treatment replicates. *** This submission represents the microarray component of the study
Project description:To study a hybrid weakness of rice, we have employed microarray expression profiling as a discovery platform to identify genes increased or decreased their expression specifically in the hybrid. Expression profiles of ‘Nipponbare’, ‘Jamaica’, and F1 hybrid were analyzed with ‘Rice oligo microarray kit’ of Agilent Technologies. Overall design: ‘Nipponbare’, ‘Jamaica’, and F1 hybrid were used for analysis. Plants were aseptically germinated and cultivated on MS medium at 25˚C. After two weeks cultivation, roots were frozen and used for measurement. Three or four independent experiments were performed at each cultivar using different plant individuals.
Project description:The present study quantifies the transcriptomes of wild-type and transgenic Ubi::OsYHB rice seedlings (in the genetic background of Oryza sativa ssp. japonica CV Nipponbare) grown in the dark or under continous red light (Rc, at 50 µmol m-2 s-1) conditions. Overall design: WT (Nipponbare cultivar; Nip) and Ubi::OsYHB/Nip transgenic seedlings were grown at 28°C for 5 days in darkness or under continuous red light at 50 µmol m-2 s-1 (Rc50). Seedlings were harvested in subjective morning, immediately frozen in liquid nitrogen and strored at -80°C until RNA extraction. The expression of OsYHB is driven by the maize Ubiquitin promoter. Two biological replicates for each treatment. Two independent, genetically single-insertion, homozygous Ubi::OsYHB/Nip lines (#1 and # 9, with determined 41- and 23-fold overexpression levels of OsYHB in comparison to the wild-type control, respectively) were used. GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA.
Project description:In this study a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with these endoparastic root nematodes with very different modes of action. Root knot nematodes induce major developmental reprogramming of the root tip, where they force the cortical cells to form multinucleate giant cells, resulting in gall-development. Our results show that root knot nematodes force the plant to produce and transfer nutrients, like sugars and amino acids, to this tissue. Migratory nematodes, on the other hand, induce the expression of proteins involved in plant death and oxidative stress, and obstruct the normal metabolic activity of the root. While migratory nematode infection also causes upregulation of biotic stress-related genes early in the infection, the root knot nematodes seem to actively suppress the local defence of the plant root. This is exemplified by a downregulation of genes involved in the salicylic acid and ethylene pathways. Interestingly, hormone pathways usually involved in plant development, were strongly induced (auxin and gibberellin) or repressed (cytokinin) in the galls. In addition, thousands of novel transcriptionally active regions as well as highly expressed nematode transcripts were detected in the infected root tissues. These results uncover previously unrecognized nematode-specific expression profiles and provide an interesting starting point to study the physiological function of many yet unannotated transcripts potentially targeted by these nematodes. Overall design: 2 or 3 biological replicates of nematode infected roots and root tips and their respective controls were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)
Project description:The allene oxide synthase (AOS) branch and the hydroperoxide lyase (HPL) branch of the oxylipin pathway function in plant responses to diverse stresses and have potential cross-talks between each other in the biosynthesis and signaling regulation, but there is still an absence of direct evidence and detailed information about this communication. Here, we identified and characterized a jasmonates acid (JA) overproduction mutant, cea62, by screening the Constitutive Expression of AOS gene (cea) from rice T-DNA insertion mutant library. Map-based cloning was used to isolate the target gene as the hydroperoxide lyase OsHPL3 gene. The gene expression, HPL enzyme activity and its resulting products, (E)-2-hexenal, were all depleted in the cea62 mutant, which resulted in dramatic JA overproduction and activation of JA signaling in the mutant. Consistent with the formation of the lesion mimic phenotype and the timing of the induction for some defense responsive genes, the activation of JA biosynthesis and signaling was regulated in a developmental way, just as the way by which OsHPL3 was regulated in the wild type plant. Microarray data showed that the JA-governed defense response was greatly activated in the cea62 mutant plant and the cea62 plant obtained enhanced resistance to the bacterial blight pathogen Xanthomonasoryzaepvoryzae (Xoo) T1 strain. Wounding response was attenuated in the cea62 mutant at an early developmental stage, while it was partially recovered when JA levels were elevated at a later developmental stage in the cea62 mutant. But, the wounding response was not altered at different developmental stages in the wild type plant. These findings suggest that these two branches of the oxylipin pathways crosstalked in the biosynthesis and signaling pathways and cooperated with each other to function in diverse stress responses. We compared the gene expression profile in leaf tissues of the wild-type plant and the cea62 mutant after lesion mimic phenotype appeared two months after sowing. Total RNAs were extracted from leaf blades from the rice (Oryza sativa L.) wild-type Nipponbare plant and from leaf blades of the rice (Oryza sativa L.) cea62 mutant in the Nipponbare (ssp japonica) background at two months after sowing. Three replicates of the cea62 mutant and wild type were performed.
Project description:In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5’ and 3’ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions. Examination of non-coding RNA in 2 stages in Oryza sativa, using 454 deep sequecing
Project description:To assess further the role of CYN in relation to integument morphogenesis, gametophytic cell fate specification, embryogenesis and endosperm development, we compared the expression profiles between the cyn mutant and wild-type at two different stages(before flowering and 5 days after pollination stage) of ovule development by microarray analysis. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as auxin efflux & polarity & cell differentiation, flower and embryonic development, signal transduction.These results supported that MADS protein CYN could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes (including MADS or non-MADS transcription factors) involved in developmental and hormonal pathways. Overall design: Three independent biological replicates of cyn mutant and wild-type panicle mRNA at two different stages of ovule development were used for microarray experiments. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at before flowering and 5 days after pollination stage.
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression. Control condition experiment, root or shoot of WT vs. MIT knockdown plant. Two replicates each comparison, including a dye swap.