Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Transcriptome Analysis of Leaf Sheath Blight Response in resistant versus susceptible rice varieties

ABSTRACT: We carried out an RNA-seq based transcriptome study on two rice varieties, Cocodrie (CCDR; rice sheath blight susceptible) and MCR10277 (MCR; rice sheath blight resistant), to profile the time-series wide genome-scale transcriptional differences in response to sheath blight (SB), an infection caused by R. solanii (LR172) . Our approach is cross-referencing differentially expressed genes with significant variants of two phenotypically different varieties to validate known and discover novel variants and to further understand rice's physiological response to SB.

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Noor Al-Bader

PROVIDER: E-MTAB-6402 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq to investigate the transcriptional Response to drought stress in two Indica rice varieties Nagina22 and Nonabokra

Project description:We designed a time series experiment in order to better understand acclimation and avoidance responses of two different Indica rice varieties Nagina22, a drought tolerant, and Nonabokra, a saline tolerant.We generated RNA-Seq transcriptome data for treated and untreated samples, with three biological replicates, per time point for drought response, an environmental stress experiment.The data generated was analyzed by calling polymorphisms, expression levels and eventually curate gene network pathways specific to the landraces’ genetic background and tolerance level.

2022-12-02 | E-MTAB-7317 | biostudies-arrayexpress

Intron retention and down-expression of defense response-related genes together affect the susceptibility of mutants pls4 to rice sheath bligh

Project description:Pls4 is a gene encoding a β -ketoacyl carrier protein reductase (KAR), which is mainly involved in biological processes such as cell membrane formation. However，the role of pls4 in rice sheath blight remains unclear. Our preliminary studies showed that rice pls4 mutants were highly susceptive to sheath blight in early development stage, and insensitive in adulthood. To explore the role of this gene in the occurrence of rice sheath blight, we compared the transcriptome profiles of rice pls4 mutant and wild-type by RNA-seq. The results showed that, 2569 differentially expressed genes (DEGs), and down-regulated genes were significantly enriched in defense response related biological stress. The expression pattern significantly changed in genes related to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), which were the main two innate immunity pathways in plants. The chitinase-related genes were mainly down-regulated, while both the disease-related genes and the related genes of the WRKY gene family were significantly up-regulated. Furthermore, 467 genes had significantly alternative splicing (AS) events. Among them, intron retention (IR) affected the gene expression levels and functions in vitamin B6 (VB6) metabolism pathway, which was related to sheath blight. This suggested that IR played an important role in sheath blight resistance of mutant pls4. In conclusion, these studies suggested that pls4 might be involved in the biological stress process of sheath blight by DEGs and the fine-tuning of IR, which would provide a molecular basis for the study of rice sheath blight resistance.

2022-05-27 | GSE203661 | GEO

RNA-seq of Oryza sativa ssp. japonica rice leaf sheath from two months old seedling

Project description:The RNA-seq data was generated to identify the genes that are expressed in rice leaf sheath

2020-03-01 | E-MTAB-8353 | biostudies-arrayexpress

Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73. To find out pathways and genes involved in its high and board-spectrum resistance, microanalysis were carried out on Y73 after Xoo infection at 24 hours post inoculation (hpi). Three independant replicates were perfomed for each treatments.

2012-02-27 | E-GEOD-36093 | biostudies-arrayexpress

Transcriptomic comparative analysis of different resistance to sheath blight in rice chromosome segment substitution lines

Project description:Purpose:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of different resistance to sheath blight in rice chromosome segment substitution lines

2022-06-17 | GSE178395 | GEO

Rhizoctonia solani AG-1 IA strain:AG1 IA

Project description:Rice sheath blight genome sequencing

| PRJNA51401 | ENA

Project description:Rice transcriptome during sheath blight infection

| PRJNA818435 | ENA

rice sheath blight resistance

Project description:novel rice sheath blight resistance marker

| PRJEB28811 | ENA

Rice-xoo interaction phosphoproteome LC-MSMS

Project description:A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight at 0h and 24h after xoo infection

2015-06-29 | PXD002222 | Pride

Comparative Transcriptome Analysis of Leaf Sheath Blight Response in resistant versus susceptible rice varieties

Project description:Comparative Transcriptome Analysis of Leaf Sheath Blight Response in resistant versus susceptible rice varieties

| PRJEB24521 | ENA