Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA137987 | ENA |
REPOSITORIES: ENA
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Project description:Rice, the worldM-bM-^@M-^Ys most important food crop, is attacked by multiple herbivores and pathogens.the rice striped stem borer (SSB) Chilo suppressalis is one of another most important rice insect pests. Here, we use Affymetrix Whole-Genome rice arrays to detect SSB infestation responsive genes. RNA samples from five damaged stems of SSB-challenged 24 h rice plants or five stems from unchallenged plants (for control samples) were used to array analysis. Two replicate biological experiments of SSB treatment rice arrays and one control samples array were peformed.
2011-03-18 | E-GEOD-28012 | biostudies-arrayexpress
Project description:Rice, the world’s most important food crop, is attacked by multiple herbivores and pathogens.the rice striped stem borer (SSB) Chilo suppressalis is one of another most important rice insect pests. Here, we use Affymetrix Whole-Genome rice arrays to detect SSB infestation responsive genes.
2011-03-18 | GSE28012 | GEO
Project description:To explore the molecular mechanisms underlying the rice plant-mediated interaction between brown planthopper (BPH) and striped stem borer (SSB), gene expression changes in rice plant response to infestation by SSB, BPH or both and control were analyzed by RNA-seq.
2021-02-28 | GSE167872 | GEO
Project description:LongSAGE library in this series are from 'Whole Genome Analysis of Pathogen-Host Recognition and Subsequent Responses in the Rice Blast Patho-System' project. This work is supported by NSF-PGRP #0115642. Keywords: other
2004-11-08 | GSE1924 | GEO
Project description:Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to observe the response of two wild rice species (Oryza barthii and O. glaberrima) and two O. sativa genotypes (cv. Nipponbare and f. spontanea) to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, chlorophyll concentration and fluorescence showed that the wild species present higher level of leaf damage, increased accumulation of H2O2 and lower photosynthetic capacity when compared to O. sativa genotypes under infested conditions. Infestation decreased tiller number, except in Nipponbare. Infestation also caused the death of wild plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa genotypes, the number of panicles per plant was affected only in f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) genotypes under control and infested conditions. O. barthii has a less abundant antioxidant arsenal and is unable to modulate proteins involved with general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes and energy production, suggesting that, under infested condition, the primary metabolism is maintained more active compared to O. barthii. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors. These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming increased tolerance to mite infestation.
2021-09-09 | PXD020940 | Pride
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:The histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could eThe histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could enhance gene transcription involved in stress-responsive gene expression. The physiological and molecular mechanisms underlying plant responses to insects are being increasingly studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of transcription of hidden genes in plants damaged by insects remain largely unknown. In current study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-seq). RNA-seq data revealed that 3269 and 4609 genes were up-regulated at 3 h and 12 h after infestation with FAW, respectively. ChIP-Seq analysis revealed 1617 and 2617 genes modified by H3K9ac in rice infested with FAW at 3 h and 12 h, respectively, and H3K9ac was mainly enriched in the transcription start sites of genes.
2024-05-31 | GSE232269 | GEO
Project description:Brown planthopper (BPH; Nilaparvata lugens) is a phloem feeding insect which is one of the most serious threats to rice crops in many countries throughout Asia. 1H NMR spectroscopy, combined with chemometrics, was used to analyze the polar metabolome from leaf extracts of Thai Jasmine rice (brown planthopper (BPH)-susceptible KD) and its BPH resistant isogenic lines (BPH-resistant IL7 and BPH-resistant+ IL308 varieties) with and without BPH infestation at various time points (days 1, 2, 3, 4 and 8). Physiological changes of the rice isogenic lines were different based on the quantitative trait loci of BPH resistance. Multivariate models were capable of distinguishing between the susceptible and the resistant rice varieties throughout the infestation. The concentration of 10 metabolites were significantly altered (p < 0.05) between the infested and the control groups of each examined rice variety. Metabolic pathway analysis suggested that BPH infestation could perturb transamination during the early stages of infestation (days 1–3) for all rice varieties. In addition, the IL7 and IL308 varieties responded earlier (day 3) than the KD variety (day 8) by perturbing amino acid metabolism, shikimate and gluconeogenesis pathways. By day 8 of the infestation, the KD cultivar responded by activating the amino acid-mediated-de novo pathway whereas the IL308 variety activated the purine and pyrimidine compound-mediated-salvage pathway for nucleotide biosynthesis. This study has identified, for the first time, several potential metabolic pathways for acclimatization and defense mechanisms against BPH infestation. These findings provide a valuable, first insight into BPH resistance mechanisms in Thai Jasmine rice.
2016-11-25 | MTBLS151 | MetaboLights
Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress