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Microarray data from aerial tissue of submergence tolerant M202(Sub1) and intolerant M202

ABSTRACT: An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level.

ORGANISM(S): Oryza sativa

PROVIDER: GSE18930 | GEO | 2010/02/04

SECONDARY ACCESSION(S): PRJNA121039

REPOSITORIES: GEO

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Microarray data from aerial tissue of submergence tolerant M202(Sub1) and intolerant M202

Project description:An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level. Aerial tissue of 14-d-old plants which were submerged for 24 h were subjected to RNA extraction and hybridization on Affymetrix microarrays. Non-submerged plants were used as control. Two independent biological replicates were analyzed for each treatment/genotype.

2010-02-22 | E-GEOD-18930 | biostudies-arrayexpress

The Submergence Tolerance Regulator Sub1A Mediates Stress-responsive Expression of AP2/ERF Transcription Factors

Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response

2010-03-09 | GSE17704 | GEO

The Submergence Tolerance Regulator Sub1A Mediates Stress-responsive Expression of AP2/ERF Transcription Factors

2010-03-08 | E-GEOD-17704 | biostudies-arrayexpress

Expression data from Arabidopsis Col-0 expressing FLAG-SUB1A or FLAG-SUB1C rice ERFs

2011-05-02 | GSE27669 | GEO

Expression data from Arabidopsis Col-0 expressing FLAG-SUB1A or FLAG-SUB1C rice ERFs

Project description:In rice (Oryza sativa L.), the haplotype at the multigenic SUBMERGENCE 1 (SUB1) locus determines survival of prolonged submergence. SUB1 encodes two or three group VII Ethylene Response Factor (ERF) family transcription factors, SUB1A, SUB1B and SUB1C. A highly submergence-inducible SUB1A allele is present in lines that are submergence tolerant. This gene is the determinant of submergence tolerance. Here, the heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was employed to assess the transcriptional network mobilized by ectopic expression of SUB1A and SUB1C. Arabidopsis thaliana Col-0 plants were stably transformed with constructs allowing the expression of 35S:FLAG-SUB1A and 35S:FLAG-SUB1C. Affymetrix ATH1 arrays were hybridized with RNA isolated from 7-day-old whole seedlings at midday (growth chamber, 0.5X MS-agar plates, 1 %(w/v) sucrose, 23 ºC, 16 h light/ 8 h dark, 125 uE m-2 s-1). Two biological replicates each.

2011-05-02 | E-GEOD-27669 | biostudies-arrayexpress

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

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

mRNA sequencing of whole 15 d old Oryza sativa shoots

Project description:The rice gene SUB1A-1 confers flooding tolerance restricting shoot growth during submergence. Rice with SUB1A also show more rapid recovery after submergence ends, but mechanisms by which SUB1A improves recovery from submergence had not been examined. In this study, the transcriptome was sequenced at five time points over a 24 hour submergence recovery period in near-isogenic rice genotypes with and without SUB1A.

2017-09-01 | GSE102494 | GEO

Transcriptional 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. Keywords: Mechanism of submergence tolerance

2007-11-24 | GSE6362 | GEO

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

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