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Global expression analysis of differential expression of genes working under Soil Water Stress condition in different genotypes of rice in Vegetative and Grain-filling stage [set 2]

ABSTRACT: One of the serious constraints to realize high level of rice crop productivity in agriculture has been due to Soil Water Stress (SWS) situation that growing plants often face. In order to increase or maintain the crop productivity in SWS situation, our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SWS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogon and three Oryza sativa indica cultivars namely Nagina-22, IR20 and Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SWS condition [GSE49364 and the current study]. Global analysis of transcript profiling under SWS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the expression profiles from five rice genotypes during vegetative (Veg) and grain-filling (GF) stages under varying water conditions, viz. Before Stress (BS), After Stress (AS) and After Recovery (AR).

ORGANISM(S): Oryza sativa

PROVIDER: GSE63718 | GEO | 2016/04/01

SECONDARY ACCESSION(S): PRJNA268875

REPOSITORIES: GEO

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Global expression analysis of differential expression of genes working under Soil Water Stress condition in different genotypes of rice in Vegetative and Grain-filling stage [set 1]

Project description:One of the serious constraints to realize high level of rice crop productivity in Indian agriculture has been due to soil moisture stress (SMS) situation that growing plants often face. In order to increase or maintain the crop productivity in SMS situation our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SMS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogan and three Indian cultivar namely Oryza Nagina-22, Oryza IR20 and Oryza Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SMS condition. Global analysis of transcript profiling under SMS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the transcript profiling from five genotypes of rice under control, soil moisture stress and after recovery conditions during vegetative and grainfilling phase.Here in case of Nagina-22 we have taken grainfilling stage.

2016-04-01 | GSE49364 | GEO

Transcript profiling of drought responsiveness in two contrasting rice genotypes during vegetative stage stress

Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought 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 control and drought stressed conditions during vegetative phase. Keywords: Drought response We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during drought stress. We used two contrasting rice genotypes (IR64 drought susceptible and Apo drought tolerant) differing in their degree of drought tolerance. Plants were grown under green house conditions and drought stress was imposed on 33rd DAS. Leaf sampling was done in both control and drought stressed plants after 6 days of drought stress. Three replications of microarray experiments were carried out by hybridizing the control samples against the drought stressed samples.

2012-04-30 | E-GEOD-5978 | biostudies-arrayexpress

Transcript profiling of drought responsiveness in two contrasting rice genotypes during vegetative stage stress

2012-05-01 | GSE5978 | GEO

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.

2012-04-30 | E-GEOD-37650 | biostudies-arrayexpress

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2013-08-20 | GSE49963 | GEO

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2012-05-01 | GSE37650 | GEO

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

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2016-04-18 | GSE48346 | GEO

Polysome bound mRNA Seq analysis of tolerant (APO) and susceptible (IR64) variety of Oryza sativa cv. Indica under 50% drought

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2024-03-20 | GSE232522 | GEO

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2013-08-20 | E-GEOD-49963 | biostudies-arrayexpress

Master regulators of oxidative stress associated genes improves stress adaptation in rice

Project description:Microarray data of contrasting genotypes were performed between control and stress conditions. Please cite the following work, if you are using the data Sujitha, D., Kumar, H.G.J., Thapliayal, G. et al. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.). Plant Biotechnol Rep (2023). https://doi.org/10.1007/s11816-023-00819-8

2023-02-13 | GSE181763 | GEO

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