Oryza
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR128976_1.fastq.gz | Fastqsanger.gz | |||
| DRR128976_2.fastq.gz | Fastqsanger.gz | |||
| DRR128977_1.fastq.gz | Fastqsanger.gz | |||
| DRR128977_2.fastq.gz | Fastqsanger.gz | |||
| DRR128978_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Studies have shown that Rice Salt Sensitive 1 (RSS1) is involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RSS1. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
2017-12-31 | E-MTAB-5583 | biostudies-arrayexpress
Project description:Studies have shown that Respiratory Burst Oxidase Homolog B (RBOHB) are involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RBOHB. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
2017-12-31 | E-MTAB-5560 | biostudies-arrayexpress
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
Project description:Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice (Oryza sativa L. ssp. japonica and indica) to drought stress at the late vegetative stage and harvested leaves for protein extraction and subsequent label-free shotgun proteomics. Gene ontology analysis revealed some differentially expressed proteins were induced by drought in all eight genotypes; we speculate that these play a universal role in drought tolerance. However, some highly genotype-specific patterns of response to drought suggest that some mechanisms of metabolic reprogramming are not universal. Such proteins had largely uncharacterized functions, making them biomarker candidates for drought tolerance screens.
2020-01-17 | PXD016150 | Pride
Project description:Changes in patterns of gene expression are believed to be responsible for the phenotypic differences within and between species. Although the evolutionary significance of functional mutations has been emphasized in rice domestication, little is known about the differences in gene regulation underlying the phenotypic diversification among rice varieties. MicroRNAs (miRNAs) are small regulatory RNAs that play crucial roles in regulating post-transcriptional gene expression. Here, we studied the variation in the expression of both miRNAs and mRNA transcripts in three indica and three japonica rice varieties using RNA sequencing (RNA-seq) to examine the miRNA regulatory effect on target gene expression in rice. In total, 71.0%, 9.2%, and 1.5% of the expressed mature miRNAs showed tissue, subspecies, and tissue-subspecies interaction-biased expression. Most of these differentially expressed miRNAs are evolutionarily weakly conserved. To examine the miRNA regulatory effect on global gene expression under endogenous conditions, we performed pair-wise correlation coefficient analyses on the expression levels of 240 mature miRNAs and 1178 messenger RNAs (mRNAs) both globally and for each specific miRNA-mRNA pair. We found that the deeply conserved miRNAs can significantly decrease the target mRNA abundance. In addition, a total of 109 miRNA-mRNA pairs were identified as significantly correlated pairs (Adjusted p<0.01). Of those, 41 pairs showed positive correlations, while 68 pairs showed negative correlations. Functional analysis elucidated that these mRNAs belonged to different biological pathways that could regulate the stress response, metabolic processes, and rice development. In conclusion, the joint interrogation of miRNA and mRNA expression profiles in this study proved useful for the study of the role of miRNA expression and regulation in the plant transcriptome.
2017-02-09 | GSE71925 | 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:Whole genome sequencing project of Japanese rice varieties
| PRJDB8365 | ENA
Project description:Genome sequencing project of japonica rice varieties
| PRJDB4518 | ENA
Project description:sequence variation among rice varieties
| PRJDB6805 | ENA
Project description:Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling researchers to visualise the sites alongside other stored data on rice proteins, including structural models from AlphaFold2, and into PeptideAtlas, enabling visualisation of the source evidence for each site, including scores and source mass spectra. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation caused by different kinase groups. We cross-referenced phosphosites against single amino acid variation (SAAV) data sourced from the rice 3000 genomes data, to identify SAAVs within or proximal to phosphosites that could cause loss of a particular site in a given rice variety. The data was further clustered to identify groups of sites with similar patterns across rice family groups, allowing us to identify sites highly conserved in Japonica, but mostly absent in, for example, Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties.
2023-11-08 | PXD046188 | Pride