Differential expression of Rice genes upon Rhodotorula treatment
ABSTRACT: The experiments were performed to understand the molecular basis of plant growth promotion in rice by Rhodotorula mucilaginosa JGTA-S1, an endophytic yeast from Typha angustifolia Three week old rice plant grown in untreated condition were supplemented with Rhodototorula cell suspension. Shoots were harvested 0hr, 6hrs or 24hrs post treatment. Total RNA isolated from those shoot tissue & used for Microarray. 0 hr treated sample considered here as Control
Project description:The experiments were performed to understand the molecular basis of plant growth promotion in rice by Rhodotorula mucilaginosa JGTA-S1, an endophytic yeast from Typha angustifolia Overall design: Three week old rice plant grown in untreated condition were supplemented with Rhodototorula cell suspension. Shoots were harvested 0hr, 6hrs or 24hrs post treatment. Total RNA isolated from those shoot tissue & used for Microarray. 0 hr treated sample considered here as Control
Project description:Plant organ formation, or organogenesis is the process in which the primordium derived from shoot apical meristem develops into an organ with a given shape and proper function, through a series of cell division and differentiation. To decipher the genetic program underling plant organ formation, we targeted early rice stamen development that covers most important events in male organ formation and germ cell initiation in plants. Totally, seven samples were used in this experiment. Stamens of stages 2-6 was collected through microdissection under microscope. And to ensure the stamen primordia collected are at corresponding stages, rice panicles were cut in half longitudinally, one half for paraffin sectioning to confirm developmental stages and the other half for preparing GEP samples. Samples of primordial and just-expanded third leaves were used as controls because leaf and stamen are homolog organs. RNA was extracted and amplified with Two-Cycle Eukaryotic Target Labeling Assay kit, and then hybridized to microarrays. Three biological replicates were applied for each sample.
Project description:Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed. We compared and anylyzed the transcriptome changes of the bacteria Bacillus subtilis OKB105 in response to rice seedings for 2 h. Total RNA was extracted and Random priming cDNA synthesis, cDNA fragmentation and terminal labeling with biotinylated GeneChip DNA labeling reagent, and hybridization to the Affymetrix GeneChip Bacillus subtilis Genome Array.
Project description:H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoagland’s medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.
Project description:Micro-RNA associated with low-N tolerance have been identified in rice (Oryza sativa) genotypes on the basis of differential expression of miRNA in low-N tolerant and low-N sensitive genotypes of rice. Since, miRNAs emerged as key players in plant responses and adaptation to stress, identification of low-N responsive miRNAs and their targets could help to uncover the molecular mechanisms of N-deficiency tolerance in plants. We used affymetrix based GeneChip miRNA_2.0 Array to detail the global programme of miRNA expression variation in low-N tolerant (IC-547557) and low -N sensitive (Vivek Dhan). Low-N tolerant and low-N sensitive rice genotypes were grown using the nutrient medium containing 2 mM K2SO4, 2 mM MgSO4, 1 mM CaCl2, 0.3 mM NaH2PO4, 40 µM Fe-EDTA, 9 µM MnCl2, 25 µM Na2MoO4, 20 µM H3BO3, 1.5 µM ZnSO4, and 1.5 µM CuSO4. The nitrogen in the form of NH4NO3 was maintained as 0.01 mM (low-N condition). The pH of the nutrient solutions was adjusted to 6.0 and the solutions were changed every three days. Twenty-day-old plants were sampled for expression studies of miRNA.
Project description:Comparative transcriptome was profiled of rice seedling shoots in responding to live S. meliloti1021(LS) and dead S. meliloti1021 (DS) inoculation. The shoots with LS and DS were collected at 1, 2, 5 and 8 DAI respectively for microarry analysis. A total of 2413 differentially expressed genes (DEGs) were detected (q ≤ 0.05 and 1.5-fold change used as a cutoff), showing significantly differences between LS and DS. Enriched gene ontology terms and pathways analysis indicated that functions of these DEGs were observably involved in biotic stress, cellular regulation, plant hormone transduction, cell cycle and cell division. Among the classes of transcription factors, some key regulatory gene families such as WRKYs, NAC, bZIP, MYB and ZIM were involved in responding to defense. Others such as AUX, E2F/DP, BES1 and GASR were growth related. We used microarrays to profile the global view of gene expression underlying S. meliloti 1021 inoculation and identified regulated plant genes and pathway that likely key events in endophytic colonization and molecular promotion mechanism. Surface sterilized seeds were germinated in petri plates with distilled water in the dark for 3 days at 28°C. And then transferred aseptically into sterilized glass bottle, which containing 175 cm3 of sterile vermiculite and 100 mL of 1/4 Kimura B solution. After 2 days transferred to sterilized glass bottle, the seedling were inoculation with live S. meliloti1021 (LS) as treatment and dead S. meliloti1021 (DS) as control. Shoots from inoculated by live S. meliloti1021 (LS) and dead bacteria as control (DS) were collected at 1, 2, 5 and 8 DAI respectively. Every RNA sample was derived from 5 independent seedlings. In sum, four time points were selected and three biological replicates were performed, totally 24 rice genome arrays were used.
Project description:We used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Typha angustifolia under control and cadmium stressed condition. A total of 114 conserved miRNAs and 41 novel candidate miRNAs encoded by 66 hairpin precursors were identified in both small RNA libraries. 4 conserved and 6 novel miRNAs showed specific expression, which, combined with function of target genes, suggests that miRNAs may play a role in plant Cd stress response.These results provide a framework for further analysis of miRNAs and their role in regulating Typha angustifolia response to cadmium stress. Overall design: Two small RNA libraries, with (Cd) and without (CK) cadmium-treatment, were sequenced by Illumina sequencing technology
Project description:Expression profiling of lumbar spinal cord from MLC/SOD1G93A mice and age matched controls at 120 days of age. We used Affymetrix GeneChip Mouse Gene expression 2.0 st Array to determine differential gene expression. Samples were collected from mice MLC/SOD1G93A and controls FVB age matched at 4 month-old. Samples were collected representing each genotype and age group for RNA extraction and hybridization on Affymetrix Microarrays.
Project description:Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2). Leaf tissues of 6-week-old LRK1 060615 transgenic rice and control 9311 rice (10 plants each) were selected.
Project description:Whole transcriptome sequencing of B. phytofirmans PsJN colonizing potato (Solanum tuberosum L.) plants was used to analyze in planta gene activity and in the response of strain PsJN to plant stress in three different time points. The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded on the genome of strain PsJN. Our study indicates that endophytic B. phytofirmans PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress, it senses plant stress signals and adjusts its gene expression accordingly.