Oryza sativa Indica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377880 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5311320.fastq.gz | Fastqsanger.gz | |||
| SRR5311330.fastq.gz | Fastqsanger.gz | |||
| SRR5311340.fastq.gz | Fastqsanger.gz | |||
| SRR5311321.fastq.gz | Fastqsanger.gz | |||
| SRR5311331.fastq.gz | Fastqsanger.gz |
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Project description: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. Keywords: Bacterial leaf blight disease resistance mechanism
2007-10-29 | GSE6244 | GEO
Project description: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.
2008-06-14 | E-GEOD-6244 | biostudies-arrayexpress
Project description:An indica rice cultivar FR13A, is widely grown as submergence tolerant variety and can withstand submergence up to two weeks. The tolerance is governed by a major QTL on chromosome 9 and represented as sub1. Recently the gene for sub1 has been mapped and cloned. However, the trait is governed by several QTLs and not by a single gene. To understand the mechanism of submergence tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype 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 constitutive and submerged conditions at seedling stage. SUBMITTER_CITATION: Combining In Silico Mapping and Arraying: an Approach to Identifying Common Candidate Genes for Submergence Tolerance and Resistance to Bacterial Leaf Blight in Rice. Mol. Cells 2007 24:394-408. Experiment Overall Design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during submergence treatment. We used two contrasting rice genotypes (FR13A tolerant and IR24 susceptible) differing in submergence response. Plants were grown in growth chambers and treated by submerging the plants in transparent polythene bags on14th DAS. Leaf sampling was done in both constitutive and treated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the RNA from tolerant samples against the susceptible lines.
2008-06-14 | E-GEOD-6362 | biostudies-arrayexpress
Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.
2012-02-27 | GSE36093 | GEO
Project description:Accumulating information indicates that plant disease resistance signaling pathway frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, functions as a convergent point of the crosstalk between pathogen-induced salicylate-dependent defense pathway and at least five other physiological pathways. Genome-wide analysis of the expression profiling of OsWRKY13-overexpressing lines showed that OsWRKY13 directly or indirectly regulates the expression of more than 500 genes, which are potentially involved in different physiological processes according to the classification of Gene Ontology database. Comparing the expression patterns of genes functioning in known pathways or cellular processes upon pathogen infection and the phenotypes between OsWRKY13-overexpressing and susceptible wild-type plants, we find that OsWRKY13 is also regulator of other physiological processes during pathogen infection. OsWRKY13-involved disease resistance pathway synergistically interacts with glutathione/glutaredoxin system and flavonoid biosynthesis pathway via OsWRKY13 to monitor redox homeostasis and may enhance the biosynthesis of antimicrobial flavonoid phytoalexins. Meanwhile, OsWRKY13-invloved disease resistance pathway antagonistically interacts with SNAC1-mediated abiotic-stress defense pathway, JA signaling pathway, and terpenoid metabolism pathway via OsWRKY13 to suppress salt and cold defense responses as well as may retard rice growth and development. Keywords: abiotic stress, bacterial blight, microarray, Oryza sativa, signal transduction, WRKY transcription factor
2008-07-02 | GSE8380 | GEO
Project description:Environmental stresses influence the growth of plants and the productivity of crops. Salinity is one of the most important abiotic stresses for agricultural crops. PCD is induced by various biotic and abiotic stresses in algae and higher plants, including high salinity treatment. OsPDCD5, an ortholog to mammalian-programmed cell death 5, is up-regulated under low temperature and NaCl treatments. We found that the transgenic rice which constitutively expressed anti-OsPDCD5 increased salt stress tolerance in unique ways. By using the Rice Genome Microarray, we identified target genes that were regulated in transgenic rice plants by anti-OsPDCD5.
2011-11-01 | GSE28209 | GEO
Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73. To find out pathways and genes involved in its high and board-spectrum resistance, microanalysis were carried out on Y73 after Xoo infection at 24 hours post inoculation (hpi). Three independant replicates were perfomed for each treatments.
2012-02-27 | E-GEOD-36093 | biostudies-arrayexpress
Project description:Comparative analysis of rice plants infected with Rice tungro bacilliform virus
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Project description:Heat stress along with other abiotic stresses is one of the major factors affecting crop health and overall yield in a tropical country like India. Thus, there is an urgent need to understand the dynamics of heat responsiveness at the molecular as well as physiological level. Fortunately, India has a number of indigenous varieties that show tolerance to extremes in temperature during the scorching summer months. The cultivar Annapurna is a fast growing dwarf variety of rice that is heat tolerant while the most widely grown indica rice in South and Southeast Asia, IR64, is susceptible to high temperatures. These two cultivars present an excellent opportunity to study the differences in response to heat stress, and, thereby help in elucidating the genes involved in conferring tolerance to high temperature. The present study involves transcript profiling of the two cultivars, Annapurna (tolerant) and IR64 (susceptible) under both control and heat stressed conditions.
2021-07-26 | GSE41648 | GEO
Project description:Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).
2017-09-06 | GSE103480 | GEO