Oryza sativa
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ABSTRACT:
PROVIDER: PRJDB35993 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a major insect pest of cultivated rice in temperate Asia. GRH2-near-isogenic line (NIL) TGRH11, GRH4-NIL (TGRH16) and GRH2/GRH4-pyramided line (PYL) TGRH29 were developed by introducing the GRH2 and GRH4 from indica rice (DV85). We identified GRH-inducible genes in respective rice lines. Furthermore, we compared the gene expression levels between NILs/PYL and control plants (T65).
2016-04-02 | GSE46409 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to investigate NGS-derived rice leaf transcriptome profiling (RNA-seq) exposed to green rice leafhopper (GRH) and validated RNA-Seq results using quantitative reverse transcription polymerase chain reaction (qRT–PCR). Methods: Rice leaf mRNA profiles of 21-day-old wild-type (WT) and Near Isogenic Line (NIL) rice were generated by deep sequencing, in triplicate, using Illumina’s HiSeq™ 4000 Sequencing System. For assembled genes, longest contigs of the assembled contigs were filtered and clustered into the non-redundant transcripts using CD-HIT-EST (Li et al., 2001; Bolger et al., 2014). qRT–PCR validation was performed using ROX and SYBR Green assays. Results: RNA-Seq results revealed that an average of 1,766,347 (1,240,317 in control and 526,030 GRH treated plants) and 3,676,765 (2,986,748 control and 690,017 GRH) counts per million mapped (CPM) reads were generated from Ilpum and NIL GRH treated plants, respectively. After alignment, more than 75% of all reads were successfully mapped to the reference genome, and 8,859 genes and 15,815,400 transcripts were obtained. GRH infestation caused differential expression of 4265 up-regulated and 4,594 down-regulated genes in Ilpum, while in NIL, 4,479 and 4,380 genes were up- and down-regulated, respectively 48 h post-infestation. A total of 3,424 differentially expressed genes (DEGs, 1,605 up-regulated in Ilpum and down-regulated in NIL; 1,819 genes up-regulated in NIL and down-regulated in Ilpum) were identified. Interestingly, these DEGs were found to be involved in key physiological processes, with interesting molecular functions, including plant defense against diverse biotic stresses, hormone signaling, and other developmental processes. Based on the quantile normalization of the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values followed by student’s t-test (p <0.05) we identified 3,283 DEGs in Ilpum (1,935 upregulated and 1,348 downregulated) and 2,599 DEGs in NIL (1,621 up-regulated and 978 down-regulated) with at least log2 (logarithm base 2) 2-fold change (Log2FC) in expression upon GRH infestation. Conclusions: The current study has provided the first RNA-Seq dataset and comparative transcriptome profile of GRH responsive genes from Ilpum (GRH-susceptible rice cultivar) and a near isogenic line (NIL) carrying Grh1 gene introduced from Shingwang into Ilpum to investigate the possible transcriptional interaction with other defense related genes. In addition, RNA-Seq data and MapMan analysis revealed the activation of multiple regulatory pathways following GRH infestation. Furthermore, the observed differential transcriptome profile between Ilpum and NIL would suggest the existence of a possible interaction network between Grh1 and other defense related genes towards GRH resistance in rice.
2021-06-10 | GSE176497 | GEO
Project description:Drought is a major environmental constraint affecting physiological, biochemical and molecular changes of crops, causing loss in crop productivities. Understanding the molecular mechanisms of drought tolerance is important for crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, Rice outermost cell-specific gene 10 (Roc10), improves drought tolerance and grain yield by increasing lignin accumulation in ground tissues of rice plants. Overexpression of Roc10 significantly enhanced drought tolerance of transgenic rice plants at the vegetative stages of growth with highly effective photosystem and reduction of water loss rate as compared with non-transgenic control and RNAi plants. More importantly, Roc10 overexpression plants had higher drought tolerance at the reproductive stage of growth with higher grain yield over controls under field-drought conditions. We identified downstream and putative target genes of Roc10 by using RNA-seq and ChIP-seq data of rice shoots. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots with a concomitant increase in accumulation of lignin. The overexpression and RNAi lines showed opposite patterns of lignin accumulation. The Roc10 is mainly expressed in the outer cell layers including epidermis and vasculature of shoots that coincides with areas of increased lignification. Furthermore, the Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggested that the Roc10 confers drought stress tolerance by enhancing lignin biosynthesis in ground tissues of rice plants.
2018-01-06 | GSE93288 | GEO
Project description:In order to investigate the roles of ScOYE3, an old yellow enzyme gene from Saccharomyces cerevisiae, in detoxification and phytoremediation of 2-Nitroaniline (2-NA) in rice, we employed the RNA-seq approach to identify differentially expressed genes in 2-NA-treated wild-type (ZH11) rice plants and transgenic (OE1) rice plants overexpressing ScOYE3. Processing of RNA samples on the Illumina HiSeq 4000 system yielded more than 50 million reads, each 100bp in length, encompassing 6.28Gb of sequence data for each sample which was then mapped to the reference genome. Quantitative analysis of RNA-seq data identified substantial variation in expression profiles among different genotypes, consistent with known functional differences. Transcript abundance obtained from RNA-seq data was indicated as TPMs and therefore, Up- and down-regulated genes were determined by a greater than 2-fold change of normalized TPMs (padjust<0.05) in comparison analysis.
2024-01-01 | GSE201399 | GEO
Project description:This study aims to deal with a comparative proteome analysis of shoot and root tissues of contrasting phosphorus (P) responsive rice genotypes (Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL). Proteins were isolated from shoot and root tissues collected from 45-day-old rice plants grown hydroponically in PusaRicH medium with P (16ppm, +P) or without P (0 ppm, -P) under controlled environmental conditions. Following protein quantification using the Bradford method, and quality check using 1D SDS-PAGE, trypsin was used for in-solution digestion and Nano ACQUITY UPLC-MS/MS was used to separate and identify peptides. This study aimed at deciphering the molecular aspect of Pup1 QTL in P-starvation stress tolerance in rice.
2023-02-27 | PXD039084 | Pride
Project description:Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA). Whole genome expression maps of rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).
2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress