Oryza sativa Japonica Group
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REPOSITORIES: ENA
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Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.
2023-01-02 | GSE196229 | GEO
Project description:Whole WRKY gene family transcription analysis in rice during biotic and abiotic stress.
| PRJNA97207 | ENA
Project description:Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 µM Cd for 24 hours. In total, ~60,000 transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated and ~36,000 transcripts were responsive to Cd exposure. Among multigenic families that may protect cells from generated ROS and reduce Cd toxicity, prominently upregulated antioxidant enzyme genes were identified. Furthermore, 168 different metal ion transporter genes, which might mediate the transport of transition Cd, responded to Cd exposure. qRT-PCR analysis of randomly selected genes indicated that their expression changed obviously after exposure to various heavy metal stresses. The Cd responsive genes included many abiotic stress (drought, high-salinity, low temperature) responsive genes. Based on further investigation into the expression patterns of abiotic stress regulatory genes such as DREB, part of the signal transduction pathway for Cd exposure was determined to cross-talk with abiotic stress signaling pathways. Our results provide useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of Cd tolerance in crop species.
2014-08-07 | E-MTAB-4306 | biostudies-arrayexpress
Project description:Seeds experience several stress responses from dry to germinated state. To determine the regulators contributing to imbibitional tolerance, dynamic transcriptome analyses were conducted at dry (0 h), imbibed (24 h) and germinated (48 h) stages in japonica Jiucaiqing in this study. Results showed that the differentially expressed genes (DEGs) were pronounced in the early stage (0-24 h) than the late stage (24-48 h); 1,452 transcripts were differentially expressed (648 up-regulated and 804 down-regulated) in the early stage and 625 transcripts (230 up-regulated and 395 down-regulated) in the late stage. Gene ontology and MapMan analyses confirmed that 391 and 164 DEGs at the early and late stage respectively involved in stress responses pathway. These DEGs included the abiotic stress-, hormone-, peroxidases-, signaling-, transcription-, proteolysis- and cell wall-related genes. Nearly all the heat stress-related DEGs, e.g. hsp20 and DnaK family proteins, were down-regulated with seed germination, while the peroxidases- and signaling-related DEGs, e.g. calcium-binding proteins, were up-regulated. Many auxins-, abscisic acid- and ethylene-related DEGs, e.g. 9-cis-epoxycarotenoid dioxygenase, OsFBL16 and OsSAUR33, were involved in stress responses during seed germination. Meanwhile, several transcription factors of bZIP and MYB, ethylene responsive element binding protein family (ERF), and heat stress transcription factor family (HSF) were identified during seed germination. The proteolysis-related DEGs, e.g. ubiquitin-related proteins, were significantly regulated during seed germination. The uniformity between transcriptome data, quantitative trait loci co-localizations and quantitative RT-PCR results confirm the crucial roles of the cell wall-related genes on seed germination. The identified stress-responsive might be useful for the improvement of imbibitional tolerance in rice.
2020-04-28 | GSE98338 | GEO
Project description:Transcriptome study of rice early response to rice blast fungus
| PRJNA178235 | ENA
Project description:To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.
2017-06-25 | GSE76415 | GEO
Project description:The inbuilt mechanisms of plant survival have been exploited for improving tolerance to abiotic stresses. We have investigated the subcellular interactions of rice stress-associated proteins (SAPs) using yeast two-hybrid and FRET approaches and found that A20 domain mediates the interaction of OsSAP1 with self, its close homolog OsSAP11, and a rice receptor-like cytoplasmic kinase, OsRLCK253. Such interactions between OsSAP1/11 and with OsRLCK253 occur at nuclear membrane, plasma membrane and in nucleus. Functionally, both OsSAP11 and OsRLCK253 could improve the water-deficit and salt stress tolerance in transgenic Arabidopsis plants via a signaling pathway affecting the expression of several common endogenous genes. The yield in transgenic plants is also protected indicating the agronomic relevance of OsSAP11 and OsRLCK253 in conferring abiotic stress tolerance. Arabidopsis transgenic plants expressing rice genes OsSAP11 and OsRLCK253 were compared with untransformed plants at seedling level
2011-05-01 | E-GEOD-27861 | biostudies-arrayexpress
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport
| PRJNA152307 | ENA
Project description:OsCBM1 gene roles in rice stress tolerance
| PRJNA516083 | ENA