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Gene expression profiling of rice embryogenic calli after Agrobacterium infection

ABSTRACT: Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChip® Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group Oryza sativa Indica Group

PROVIDER: GSE32426 | GEO | 2012/01/01

SECONDARY ACCESSION(S): PRJNA147917

REPOSITORIES: GEO

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Gene expression profiling of rice embryogenic calli after Agrobacterium infection

Project description:Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChipM-BM-. Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97. The mature embryo-derived embryogenic calli of Nipponbare (Nip) and Zhenshan 97 (ZS) were infected by Agrobacterium. Calli of Nip and ZS were sampled just before infection (0 h) and 1h, 6h, 12 h and 24h after infection, respectively. Three independent biological replications for each time point of the two varieties were used. To avoid the influence of polymorphisms between the probe sequence on the array and the genomes of the varieties used, we used a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of gDNA from Nip and ZS with the PM oligonucleotide probes on the rice array. The genomic DNA of Nip and ZS were extracted and hybridized to the Affymetrix Rice Genome Arrays. Three biological replications per cultivar were performed.

2012-01-01 | E-GEOD-32426 | biostudies-arrayexpress

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression array: Transcript and Genome Hybridizations

Project description:The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

2010-06-01 | GSE16341 | GEO

Metabolome analysis on multi-connected biparental chromosome segment substitution line populations in rice

Project description:rice flag leaves at heading stage from three chromosome substitution line populations, which were respectively constructed by introducing genomic segments from japonica cultivar Niponbare, indica cultivar Minghui 63 and wild accession ACC10, to an indica cultivar Zhenshan 97, were collected. Metabolomics profile was conducted to generate quantitative trait loci that may affect contents of metabolites, and candidate genes were assigned.

2018-08-06 | ST001031 | MetabolomicsWorkbench

Expression data from rice varieties IRAT109 and ZS97 for drought stress treatment in flag leaves

Project description:Comparative transcriptional profiling of two contrasting rice genotypes,IRAT109 (drought-resistant japonica cultivar) and ZS97 (drought-sensitive indica cultivar), under drought stress during the reproductive stage

2011-11-05 | GSE25176 | GEO

Proteome analysis of rice seeds during artificial aging treatment for understanding the role of antioxidant machinery

Project description:Seed longevity is a crucial trait in agriculture as it determines the ability of seeds to maintain viability during dry storage. However, the molecular mechanism underlying seed aging and reduced seed longevity are currently not well understood. Here we report the comparative proteome and metabolome profiling of three rice cultivars varying in aging tolerance including an aging tolerant indica cultivar Dharial, an aging sensitive japonica cultivar Ilmi, and a moderately aging tolerant cultivar A2 that was generated by crossing between Dharial and Ilmi. Results obtained from comparative proteome and metabolome profiling suggest that aged seeds of all the cultivars utilize ubiquitin proteasome-mediated protein degradation which results in the accumulation of free amino acids in Ilmi while tolerant cultivars utilize those for energy production and synthesis of heat shock proteins, especially hsp20/alpha crystallin family protein. Additionally, aging tolerant cultivar seems to activate brassinosteroid signalling and suppress jasmonate signaling to initiate a signaling cascade that allows efficient detoxification of aging induced ROS to maintain the seed longevity during aging. Taken together, these results provide an in-depth understand of aging induced changes in rice seeds.

2024-01-10 | PXD043955 | Pride

Rice stem at early stage growth: Control vs.Chromosome segment substitution lines (SLs) from a cross the Koshihikari (japonica) and Habataki (indica)

Project description:By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele.

2012-04-01 | GSE35762 | GEO

Gene expression level of six rice lineages

Project description:Towards understanding gene expression variation among related rice lineages on a genome-wide scale, we sought to assess global gene expression in the heading-stage panicle using a whole genome oligonucleotide microarray designed to represent 36,926 annotated indica genes. Using a loop-design, we interrogated gene expression patterns in six related rice lineages, including O. sativa (two Asian cultivars indica and japonica), O. nivara (Asian annual wild rice), O. rufipogon (Asian perennial wild rice) and O. glaberrima (African cultivated rice). Series_sample_order: Sample 1-12 Slide A; Sample 13-24 Slide B

2008-06-10 | E-GEOD-11712 | biostudies-arrayexpress

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. Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.

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

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed

2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed

2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress

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