Dataset Information

Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.

ABSTRACT: High ozone (O3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O3: 31.4-32.7 ppb) or filtered air (mean O3: 6.6-8.3 ppb) in small open-top chambers (sOTCs) to select O3-sensitive (indica cv Takanari) and O3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 × 44K rice oligo DNA chip. Total RNA from dry mature dehusked seeds of Takanari and Koshihikari cultivars was extracted using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment, followed by DNA microarray analysis using the established dye-swap method. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in sOTCs 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 sensitive cv Takanari and tolerant cv Koshihikari. MapMan analysis further mapped the molecular factors activated by O3, confirming Takanari is rightly classified as an O3 sensitive genotype.

SUBMITTER: Cho K

PROVIDER: S-EPMC4091349 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.

Cho Kyoungwon K Shibato Junko J Kubo Akihiro A Kohno Yoshihisa Y Satoh Kouji K Kikuchi Shoshi S Sarkar Abhijit A Agrawal Ganesh Kumar GK Rakwal Randeep R

Plant signaling & behavior 20130911 11

High ozone (O3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O3: 31.4-32.7 ppb) or filtered ...[more]

PMID: 24025514

Similar Datasets

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.

Project description:BACKGROUND:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress. RESULTS:To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress. Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize. Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves. CONCLUSIONS:These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.

Dataset Information

Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.

Publications

Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure