ABSTRACT: We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamine in rice roots. Transcriptomic analysis of rice roots revealed that the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by glutamine within 30 minutes. Total RNA from –N and Gln-treated roots (2.5 mM Gln, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.
Project description:We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamine in rice roots. Transcriptomic analysis of rice roots revealed that the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by glutamine within 30 minutes.
Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant. Wild-type rice plants and a line carrying a T-DNA insertion in the third exon of the transcription factor gene (arid mutant) were subjected to dehydration stress for 90 min. Well-watered wild-type and T-DNA insertion plants were used as controls. Total RNA was extracted from roots and subjected to expression profiling using rice Affymetrix microarrays.
Project description:Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues. 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)
Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis. Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg lM-bM-^@M-^S1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturerM-bM-^@M-^Ys instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.
Project description:In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.
Project description:Analysis of transgenic rice plants overexpressing the rice WRKY transcription factor OsWRKY53 or its phospho-mimicking mutant (OsWRKY53SD). Results provide insight into the roles of OsWRKY53 and its phosphorylation in the basal defense signaling against the rice blast fungus. Expression profiling in wild-type, OsWRKY53- or its phospho-mimicking mutant-overexpressing rice leaves infected with or without Magnaporthe Oryzae was analyzed using one-color method with four biological replicates.
Project description:Affymetrix expression analysis was used to check transcipt expression in As (V) stress. The RNA from root of six rice genotypes (BRG-12, BRG-15, BRG-20, CN1646-5, NAYANMONI and CN1646-2) was isolated after 24 hrtreatment of As (V) 0M-BM-5m and 50M-BM-5m .The rice gene chip was used for expression analysis.
Project description:Using a yeast to hybrid screen, it was found that PHO2, a key regulator of phosphate homeostasis, could interact with GIGANTEA, a key regulator of flowering time. In addition, mutant analysis revealed that both the pho2 and gi mutants shared similar phenotypes, both at the phosphate and flowering time levels. We used microarrays to analyse the effects of each mutation (pho2 or gi) on global gene expression, and assessed the proportion of genes similalry regulated in both mutants, in both shoots and roots. Wild-type (Nipponbare), pho2 and gi knock-out rice plants were grown to 21-days before harvesting root and shoot separately.
Project description:Analysis of transgenic rice overexpressing OsWRKY28, a WRKY type transcription factor. Results provide insight into the role of OsWRKY28 in the defense signaling against rice blast fungus. Expression profiling in wild-type and OsWRKY28 overexpressing rice leaves infected with or without Magnaporthe Oryzae was analyzed using one-color method with three biological replicates.
Project description:We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamate in rice roots. Transcriptomic analysis of rice roots revealed that the expression of at least 122 genes involved in metabolism, transport, signal transduction, defense, and stress responses was rapidly induced by glutamate within 30 minutes.