GRH-inducible genes in rice plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE46409 | GEO | 2016/04/02
SECONDARY ACCESSION(S): PRJNA200289
REPOSITORIES: GEO
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). The gene expression changes in respective rice lines were detected by comparison between GRH-infested and pre-infested plants. Seedlings at the second-leaf stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and shoots were collected at 30 h after GRH infestation. Detached-leaf blades at heading stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and samples were collected at 30 h after GRH infestation. For each treatment, two biological replicates were performed.
2016-04-02 | E-GEOD-46409 | biostudies-arrayexpress
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:To investigate the genetic relationship between two major grain length loci GS3 and qGL3, we developed the near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) in the background of 93-11 (gs3/qGL3) by crossing and MAS approach. Four samples was analyzed: three near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) and their background of 93-11. Every sample had three independed duplications. And the primary panicle with 3-6 cm length from the three NILs and 93-11 were used for RNA preparation and hybrid with Rice Genome OneArray Microarray (Phalanx Biotech Group).
2014-07-22 | E-GEOD-59619 | biostudies-arrayexpress
Project description:BPH9 is a gene that confers rice strong resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively. To better understand the molecular mechanism underlying resistance to BPH mediated by BPH9, we conducted a genome-wide microarray analysis of NIL-BPH9 and 9311 at the early stage of BPH infestation.
2016-10-17 | GSE80246 | GEO
Project description:Bph6 is a gene that confers rice high resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively. To better understand the molecular mechanism underlying resistance to BPH mediated by Bph6, we conducted a genome-wide microarray analysis of NIL-BPH9 and 9311 at the early stage of BPH infestation.
2016-09-03 | GSE86379 | GEO
Project description:Reproductive barriers perform a vital role during speciation1. Hybrid weakness, the poor development of hybrids compared to their parents, hinders gene exchange between different species at the postzygotic stage2,3. The molecular and evolutionary mechanisms of hybrid weakness are poorly understood2. Here, we report that two incompatible dominant loci (Hwi1 and Hwi2) involving three genes determine the high temperature-dependent expression of hybrid weakness in interspecific hybrids of rice. Hwi1 comprises two indispensable wild rice (Oryza rufipogon)-specific leucine-rich repeat receptor-like kinase (LRR-RLK) genes, 25L1 and 25L2, for inducing hybrid weakness, and the genes possibly undergo balancing selection. Hwi2, a rare allele that is predominantly distributed in indica rice (Oryza sativa), encodes a secreted putative subtilisin-like protease. Functional analysis indicated that pyramiding of Hwi1 and Hwi2 activates the autoimmune response in the basal nodes of hybrids, interrupting root formation and then impairing shoot growth, likely due to immune signal is transmitted from the basal nodes to the above-ground parts. Considering the nature of RLK activity of Hwi1 and the protease activity of Hwi2, we propose that a certain endogenous signaling molecule produced by Hwi2 is perceived by Hwi1 to activate autoimmunity through ligand-receptor signal transduction. These findings bring new insights into our understanding of reproductive isolation and may benefit rice breeding to maximally utilize invaluable genes from wild rice. We conducted microarray analysis to unravel the global changes in gene expression of a pair of NILs (nearly isogenic lines). Plants were cultivated at constant 20°C for 20 days and then shifted to constant 30°C conditions. The basal nodes of NIL(Hwi1) and NIL(hwi1) were harvested immediately before the temperature shift (set as the 0 point) or at 3, 7 or 15 days after the shift. Three biological replicates (each comprising basal nodes from 15–20 individuals) were used for each time point.
2014-01-22 | E-GEOD-54243 | biostudies-arrayexpress
Project description:To investigate the genetic relationship between two major grain length loci GS3 and qGL3, we developed the near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) in the background of 93-11 (gs3/qGL3) by crossing and MAS approach.
2014-07-22 | GSE59619 | GEO
Project description:Purpose: This study gives insight into transcriptomic dynamics and the set of important candidate acting as modules to regulate the changes in resistant NIL upon M.oryzae infection. Methods: Rice leaves were collected after M. Oryza (Mo-nwi-53) infection from resistant NILs and suceptible line were frozen in liquid nitrogen. RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). Standard Illumina protocols was used for preparing RNA sequencing libraries. Results: Around 30 million pairs of filtered 101 base paired reads were obtained for each biological replicate. Conclusions: Pathway, gene set enrichment and co-expression analysis of SDEL unique to each resistant NIL respectively decipher the common broad spectrum resistance mechanism found in resistant NIL and provide important candidate genes.
2019-12-04 | GSE117030 | GEO
Project description:Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. We show that deletion or ectopic expression of Grh causes loss or gain of DNA accessibility, respectively. However, while Grh binding is necessary for enhancer accessibility, it is insufficient to activate enhancers. Finally, we show that human Grh homologs, GRHL1/2/3, function similarly. We conclude that Grh binding is necessary and sufficient for the opening of epithelial enhancers, but not for their activation. Our data support the model that complex spatiotemporal expression patterns are controlled by regulatory hierarchies in which pioneer factors, such as Grh, establish tissue-specific accessible chromatin landscapes upon which other factors can act.
2018-06-04 | GSE108019 | GEO
Project description:We performed ChIP-seq to determine chromatin regions binding Transcription Factor GRH-1, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms.
2022-12-31 | GSE213509 | GEO