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Microarray analysis of transcriptional responses to alkali stress in two rice genotypes

ABSTRACT: To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88.

ORGANISM(S): Oryza sativa

PROVIDER: GSE45724 | GEO | 2014/05/16

SECONDARY ACCESSION(S): PRJNA196130

REPOSITORIES: GEO

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Microarray analysis of transcriptional responses to alkali stress in two rice genotypes

Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88. Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.

2014-05-16 | E-GEOD-45724 | biostudies-arrayexpress

Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress

Project description:Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis suggested the enrichment of IAR genes involved in response to various stimuli or stresses. According to KEGG pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.

2018-07-12 | GSE104928 | GEO

Transcriptome Analysis of Alkali Shock and Alkali Adaptation in Listeria monocytogenes 10403S

Project description:Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. This study compared the transcriptome patterns of alkali stressed and non alkali stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which this important pathogen adapts and/or grows during short or long-term alkali stress. Transcription profiles associated with alkali shock (AS) responses were obtained by DNA microarray analysis of mid-exponential cells suspended in pH 9 media for 15, 30 or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained by DNA microarray analysis of cells grown to mid-exponential phase in pH 9 media . Comparison of AS and AA transcription profiles with profiles from control (pH 7.0) cells identified over 2,000 genes that were differentially expressed under alkaline conditions. Rapid (15min) changes in expression included upregulation of genes encoding for multiple metabolic pathways, (including those associated with Na+/H+ antiporters), ABC transporters of functional compatible solutes such as carnitine, motility and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30min and more) responses to AS and adaptation during growth in alkaline conditions (AA), included modest changes in mRNA concentrations, and genes involved in proton export. Keywords: Time course study of gene expression response to alkaline shock and adaptation

2007-07-25 | GSE7854 | GEO

Project description:alkali tolerance rice

| PRJNA494048 | ENA

Transcriptome analysis the citrus rootstocks of Ziyang xiangcheng (Citrus junos Sieb.) and Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) under saline-alkali stress

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2018-07-06 | GSE98996 | GEO

Alkali-salinity NaHCO3-responsive mechanisms in leaves from halophyte Puccinellia tenuiflora revealed from physiological and comparative proteomic analysis

Project description:Alkali-salinity is a major abiotic stress that limits plant growth and productivity. Studying mechanisms of alkali-salinity tolerance in halophytic plants will provide valuable information for underlying plant alkali-salinity tolerance. Puccinellia tenuiflora is considered as an ideal model plant for studying the alkali-salinity tolerant mechanisms in plants. In this study, the NaHCO3-responsive molecular mechanisms in P. tenuiflora leaves were investigated using a combined physiological and proteomic approaches. Our results implied some specific NaHCO3-responsive mechanisms in leaves from P. tenuiflora. They are (1) reduction of photosynthesis attributed to the decrease of the abundance of Calvin cycle enzymes, (2) accumulation of Na+ and K+ caused ion-specific stress, (3) accumulation of proline, soluble sugar and betaine enhanced the ability of osmotic regulation, (4) diverse reactive oxygen species (ROS) scavenging mechanisms under different NaHCO3 concentrations, and (5) alternative protein synthesis and processing strategies in chloroplast and cytoplasm. All these provide important evidence for understanding NaHCO3-responsive mechanisms in P. tenuiflora.

2022-02-23 | PXD002351 | Pride

Alkali therapy protects renal function, suppresses inflammation, and modulates cellular metabolism in kidney disease

Project description:Purpose: Characterize the renal transcriptome of a chronic kidney disease model in the presence and absence of alkali therapy (bicarbonate supplementation in water) Methods: Crystal nephropathy mice were fed a calcium-free, 0.67% oxalate diet for 10 days. Control mice were fed a calcium-free diet for the same period. Afterwards, mice were fed a standard diet containing calcium for 28 days (recovery). Therapeutically treated mice ("late") received 0.2M NaHCO3 in water during the whole recovery period. An untreated group drank tap water instead. Total RNA was extracted from whole kidney samples and used for RNAseq. Results: Using a PolyA, Truseq strategy with p-value <0.05 and log2(fold change) ≥ 0.5 or ≤ - 0.5, we identified that crystallopathy altered the expression levels of 4923 transcripts. Alkali therapy normalized or attenuated the dysregulation of 795 of those genes. Alkali therapy also altered the expression of 179 transcripts in control kidneys. Conclusions: Pathway analysis identified that alkali therapy mostly restored pathways associated to inflammation and cell metabolism.

2022-04-25 | GSE179216 | GEO

Digital gene expression (DGE) of alkali-stressed cucumber leaves

Project description:Here we performed a transcriptomic study on the effect of sodium nitroprusside (SNP) on cucumber leaves under alkali stress using Solexa/Illumina's high-throughput digital gene expression (DGE) system. Two DGE libraries (from one NaHCO3-treated sample and one NaHCO3 + SNP-treated sample) were constructed, and the gene expression variations between the two samples were compared. Hundreds of differentially expressed genes were obtained by the comparison, and GO analysis of these genes suggested that many biological processes, molecular function, cellular components were related to SNPM-bM-^@M-^Ys mitigated effect on alkaline stress. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. The experiment had 2 treatments: 30 mM NaHCO3 (alkali stress treatment, indicated as Na) and 30 mM NaHCO3+100 M-NM-<M sodium nitroprusside (indicated as SNP). Samples from Na- and SNP-treated leaves, used for RNA isolation, were harvested, and the two corresponding tag libraries of samples were constructed in parallel. Illumina sequencing of transcripts from Na- and SNP-treated samples to get gene information for cucumber leaves in different treatments.

2013-11-26 | E-GEOD-42439 | biostudies-arrayexpress

saline-alkali

Project description:saline-alkali Genome sequencing and assembly

| PRJNA509045 | ENA

saline-alkali

Project description:saline-alkali Genome sequencing and assembly

| PRJNA559010 | ENA