Transcriptomics

Dataset Information

5

Transcription profiling of indica rice cultivar FR13A under submergence treatment.


ABSTRACT: 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.

SUBMITTER: Kameswara Rao Kottapalli  

PROVIDER: E-GEOD-6362 | ArrayExpress | 2008-06-14

SECONDARY ACCESSION(S): GSE6362PRJNA99575

REPOSITORIES: GEO, ArrayExpress

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Publications

Combining in silico mapping and arraying: an approach to identifying common candidate genes for submergence tolerance and resistance to bacterial leaf blight in rice.

Kottapalli Kameswara Rao KR   Satoh Kouji K   Rakwal Randeep R   Shibato Junko J   Doi Koji K   Nagata Toshifumi T   Kikuchi Shoshi S  

Molecules and cells 20071201 3


Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcr  ...[more]

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