Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen (Xoo)

ABSTRACT: An indica rice cultivar IET8585 (Ajaya), resists diverse races of the Xanthomonas oryzae pv oryzae (Xoo) pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. To further understand the mechanism of recessive and durable resistance response, two indica rice genotypes namely, i) IET8585 (Ajaya), a disease resistant indica veriety from India and ii) IR24, a bacterial leaf blight disease susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under inoculated and un-inoculated conditions during seedling stage. Experiment Overall Design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during bacterial pathogen infection. We used two contrasting rice genotypes (IET8585 (Ajaya) blb resistant IR24 blb susceptible) differing in bacterial disease response. Plants were grown growth chambers and inoculated with bacterial pathogen on 18th DAS. Leaf sampling was done in both un-inoculated and inoculated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the resistant samples against the susceptible samples.

ORGANISM(S): Oryza sativa (indica cultivar-group)

SUBMITTER: Kameswara Rao Kottapalli

PROVIDER: E-GEOD-6244 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen Xanthomonas oryzae pv oryzae.

Kottapalli Kameswara Rao KR Rakwal Randeep R Satoh Kouji K Shibato Junko J Kottapalli Pratibha P Iwahashi Hitoshi H Kikuchi Shoshi S

Plant physiology and biochemistry : PPB 20070728 10-11

An indica rice cultivar IET8585 (Ajaya) resists diverse races of the Xanthomonas oryzae pv oryzae pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. Recessive gene-mediated blb resistance mechanism is not yet clearly understood. Here we analyzed the transcriptional profile of the blb infected resistant cultivar by rice 22K oligo array. Microarray a ...[more]

PMID: 17870590

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Project description:In this study, integrated transcriptomics, proteomics and metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of two-weeks old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h. Based on the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice. Also investigated were the molecular responses in the leaves of two-weeks old rice (cv. Nipponbare) seedlings under continuous light and pure air (as a positive control for ozone exposure experiments) for a period of 24 h. Transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that continuous light and growth for 24 h also triggers a chain reaction of altered gene expressions involved in multiple cellular processes in rice, but different from those against ozone, in general. Experiment Overall Design: Ozone-treated Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure/fumigation to the ozone (0.2 ppm). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization. Experiment Overall Design: Control Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure to continuous light and pure air. Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a Standard protocol of Agilent DNA Microarray Scanner and data processing was done by Feature Extraction software Version 8.1 from Agilent Technologies.

Dataset Information

Transcription profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen (Xoo)

Publications

Transcriptional profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen Xanthomonas oryzae pv oryzae.

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