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Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence

ABSTRACT: Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence

PROVIDER: PRJNA408068 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6053400_1.fastq.gz	Fastqsanger.gz
	SRR6053400_2.fastq.gz	Fastqsanger.gz
	SRR6053392_1.fastq.gz	Fastqsanger.gz
	SRR6053392_2.fastq.gz	Fastqsanger.gz
	SRR6053393_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence

Project description:Analysis of the impact of plant growth regulators on submergence tolerance of rice at gene expression level. The hypothesis tested in the present study was that the submergence-tolerance was improved by foliar application of paclobutrazol under sumergence stress conditions.

2017-10-12 | GSE104035 | GEO

Transcriptional profiling of indica rice cultivar FR13A under submergence treatment.

2007-11-24 | GSE6362 | GEO

Transcription profiling of indica rice cultivar FR13A under submergence treatment.

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

Comparative Transcriptional Profiling of Two Rice Genotypes, FR13A and Goda Heenati, Under Submergence Stress

Project description:Most rice (Oryza sativa L.) cultivars die within several days of complete submergence, but some indica cultivars, such as FR13A, can survive up to 2 weeks of complete submergence. In FR13A, a major quantitative trait locus (QTL), named Sub1, provides mature plants with submergence tolerance. However, the Sub1 locus can not confer flooding tolerance during germination to FR13A. Another indica cultivar, Goda Heenati, shows both tolerance to flooding during germination and submergence in mature plants. It was once reported that submergence tolerance in FR13A and Goda Heenati cultivars was controlled by their respective genetic locus. These evidences indicate that tolerance to submergence in these two cultivars may involve differential mechanisms. To gain insight into their putatively differential responses to submergence stress, the Agilent rice genome 4×44 K oligonucleotide microarray was used to explore the transcriptome of FR13A and Goda Heenati under control and submergence-stressed conditions. Two-way ANOVA analysis with Benjamini-Hochberg false discovery rate demonstrated that at an overall P＜0.01 level, 2810, 8207, and 4 probes were significantly regulated for genotype, treatment, and genotype×treatment interaction, respectively. To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and unpaired t-test P value < 0.01 was uesd for both FR13A and Goda Heenati. A total of 504 probes were up-regulated and 592 probes were down-regulated in FR13A under submergence stress. In Goda Heenati, 998 probes were induced and 1186 probes were suppressed by submergence treatment.

2010-12-01 | GSE23574 | GEO

Identification of WRKY22 targets under submergence in Arabidopsis (mRNA)

Project description:We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings. The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence.

2013-07-03 | GSE40139 | GEO

Transcriptome analysis of early submergence-responsive genes in deepwater rice

Project description:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). In this research, we have searched for genes responsible for submergence escape from a deepwater rice cultivar Pin Gaew 56 (PG56).

2018-07-01 | GSE100598 | GEO

Transcriptomic responses to submergence in elongating and non-elongating leaves of rice with and without SUB1A

Project description:This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.

2022-08-01 | GSE181336 | GEO

The flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in rice seedlings established underwater

Project description:Little is known of the consequences of genetic pyramiding of abiotic stress tolerance loci in crops. In rice (Oryza sativa L.), ANAEROBIC GERMINATION1 (AG1) encodes TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 (OsTPP7) that enhances mobilization of endosperm reserves to the embryo, promoting formation of a highly elongated hollow coleoptile in seeds sown directly into shallow paddies. This trait reduces labor costs and herbicide use. SUBMERGENCE1 (SUB1) includes the ethylene-responsive transcription factor SUB1A that confers tolerance to complete submergence by dampening shoot elongation of vegetative-phase plants and enhancing regrowth upon desubmergence. As OsTPP7 and SUB1A-1 mRNAs simultaneously accumulate in shoots, we evaluated the independent contribution and interactions between these loci in rice seeded under complete submergence until the four-leaf stage (14 d). Evaluating growth, carbohydrates, and the transcriptome of shoot tissue of four near-isogenic genotypes uncovered independent and interacting effects including: (a) early enhanced coleoptile elongation by IR64(AG1); (b) precocious transition to phototrophy followed by limited elongation by IR64(SUB1); and (c) delayed phototrophy by IR64(AG1, SUB1). mRNA-sequencing highlighted time-dependent and genotype-specific regulation of mRNAs associated with energy sensing, carbohydrate catabolism, photomorphogenesis, elongation, and defense responses. Although SUB1A did not antagonize AG1 in direct seeding, seedling establishment could be negatively impacted if submergence escape does not occur before the transition to photoautotrophy, due to antithetical regulation of carbohydrate catabolism by AG1 and SUB1.

2020-07-05 | GSE136885 | GEO

TMT-based Comparative Peptidomic Analysis of Rice Seedlings under Salt Stress

Project description:A tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for the peptidomic analysis.

2023-03-11 | PXD037574 | Pride

Transcriptome profiling of contrasting rice genotypes in response to submergence during seed germination

Project description:This transcriptome experiment identified a core set of genes differentially regulated under submergence between tolerant and sensitive rice genotypes. This differential modulation of gene expressions could contribute to the level of flooding tolerance in diverse rice genotypes. Rare allele-specific gene regulations and genotype-specific adaptive mechanisms could further promote the submergence tolerance in those genotypes with extremely adaptive phenotype.

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