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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 vs Dro1-NIL

ABSTRACT: Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type) We used two rice varieties, IR64 and near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL). We performed comprehensive microarray analysis of rice root tips with auxin treatment (3h) and pre-treatment (0h) in IR64 and Dro1-NIL. Seedling root tips of IR64 and Dro1-NIL were treated with 10 M-BM-5M 2,4-D. n = 3 biological repeats (15 seedlings per repeat).

ORGANISM(S): Oryza sativa

SUBMITTER: Yusaku Uga

PROVIDER: E-GEOD-46255 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 vs Dro1-NIL

Project description:Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type)

2013-05-07 | GSE46255 | GEO

Study on the proteomic response of 5mm sections of root tips to water-deficit stress in two contrasting genotypes of rice

Project description:In this study, we analysed the proteomic response of 5mm sections of root tips to water-deficit stress in two contrasting genotypes of rice: IR64, a lowland, drought-susceptible, and shallow-rooting genotype; and Azucena, an upland, drought-tolerant, and deep-rooting genotype. Using a Partial Least Square Discriminant Analysis, we identified statistically significant differentially abundant proteins across genotypes and conditions. Analysis of biological processes led to the identification of novel proteins involved in root elongation with specific expression patterns in Azucena.

2022-08-11 | PXD033343 | Pride

Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

Project description:Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues. 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

2012-01-12 | E-GEOD-30367 | biostudies-arrayexpress

Oryza sativa

Project description:Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 vs Dro1-NIL

| PRJNA198471 | ENA

Abscission layer (AL) at the base of flower in rice using laser micro-dissection: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL

Project description:Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare. We used two rice varieties, NIL(qSH1) and Nipponbare. NIL(qSH1) is a nearly isogenic line containing the seed shattering gene qSH1. Seed shattering is easy in NIL(qSH1), but it is not in Nipponbare. So, we used some stages of young flower in NIL(qSH1) and some in Nipponbare. Four regions: 1. abscission layer region of NIL(qSH1), 2. upper abscission region of NIL(qSH1), 3. lower abscission layer region of NIL(qSH1), and 4. abscission layer region of Nipponbare. Sample experiments: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL.

2012-03-31 | E-GEOD-33409 | biostudies-arrayexpress

Gene expression analysis in response to various hormone treatments

Project description:Hormones effect various plant developmental processes by altering gene expression. The expression of several genes is regulated by plant hormones and many of these genes are regulated commonly and specifically by various hormones. We used microarrays to study the global effect of plant hormones on rice gene expression and identify the genes involved in operlapping and specific transcriptional responses. Rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in water (control) or 50 ÂµM solution of indole-3-acetic acid (auxin, IAA) and benzyl aminopurine (cytokinin, BAP) and 100 ÂµM solution of abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ethylene derivative, ACC), salicylic acid (SA) and jasmonic acid (JA) for 3h. The 5 micrograms of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Two biological replicates for each sample (two controls, IAA, BAP, ABA, ACC, SA and JA) were used for microarray analysis.

2013-12-31 | E-GEOD-37557 | biostudies-arrayexpress

Transcriptional reprogramming by root knot and migratory nematode infection in rice

Project description:In this study a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with these endoparastic root nematodes with very different modes of action. Root knot nematodes induce major developmental reprogramming of the root tip, where they force the cortical cells to form multinucleate giant cells, resulting in gall-development. Our results show that root knot nematodes force the plant to produce and transfer nutrients, like sugars and amino acids, to this tissue. Migratory nematodes, on the other hand, induce the expression of proteins involved in plant death and oxidative stress, and obstruct the normal metabolic activity of the root. While migratory nematode infection also causes upregulation of biotic stress-related genes early in the infection, the root knot nematodes seem to actively suppress the local defence of the plant root. This is exemplified by a downregulation of genes involved in the salicylic acid and ethylene pathways. Interestingly, hormone pathways usually involved in plant development, were strongly induced (auxin and gibberellin) or repressed (cytokinin) in the galls. In addition, thousands of novel transcriptionally active regions as well as highly expressed nematode transcripts were detected in the infected root tissues. These results uncover previously unrecognized nematode-specific expression profiles and provide an interesting starting point to study the physiological function of many yet unannotated transcripts potentially targeted by these nematodes. 2 or 3 biological replicates of nematode infected roots and root tips and their respective controls were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)

2013-01-10 | E-GEOD-35843 | biostudies-arrayexpress

Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

2012-01-12 | GSE30367 | GEO

Influence of Nod Factors on early developmental stages of root development in Medicago truncatula

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2016-06-01 | E-GEOD-74099 | biostudies-arrayexpress

Transcriptome profile for roots of the rice plants which showed favorable morpho-physiological adaptation when subjected to severe drought stress

Project description:To understand how OsNAM12.1 over-expression influences the target genes within qDTY12.1 and across the genome to affect root growth, the root transcriptome of Vandana, 481-B, IR64-Tr-E2, and IR64-WT were compared under control and drought conditions. Drought induced gene expression was studied in the roots of the rice plants subjected to severe drought. Seeds of Vandana, 481-B, IR64 and the OsNAM12.1 overexpression line (OsNAM Event 2) were sown in 5 biological replicates in a randomized complete block design for both the well watered and drought stress treatments.

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