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Oryza sativa

ABSTRACT: Transcriptome diversity among rice root types in salinity tolerant and sensitive varieties

PROVIDER: PRJNA388342 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5626520_1.fastq.gz	Fastqsanger.gz
	SRR5626520_2.fastq.gz	Fastqsanger.gz
	SRR5626521_1.fastq.gz	Fastqsanger.gz
	SRR5626521_2.fastq.gz	Fastqsanger.gz
	SRR5626522_1.fastq.gz	Fastqsanger.gz

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Transcriptome diversity among rice root types in salinity tolerant and sensitive varieties

Project description:Differences in gene expression were compared among nodal roots, S-type lateral roots, and L-type lateral roots of salinity tolerant and sensitive rice varieties.

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Project description:Comparative transcriptome analysis of different root types of a salinity sensitive rice cultivar under salinity stress

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Soil salinity and mechanical obstruction differentially affects embryonic root architecture in native rice varieties of West Bengal

Project description:Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.

2018-12-20 | GSE117170 | GEO

Root-specific transcriptional profiling of contrasting rice genotypes in response to salinity stress

Project description:Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Keywords: stress response

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Oryza sativa Transcriptome or Gene expression

Project description:We analyzed the transcriptome profiles for rice grain from heat-tolerant and -sensitive lines in response to high night temperatures at the early milky stage using the Illumina Sequencing method. On the 8th day after the labeled florets flowered, plants with the same label were transferred to chambers and maintained at a temperature of 38.0âÂ±â0.5Â°C (treatment) or 25.0âÂ±â0.5Â°C (control) for the dark period (10 h), and 26.0âÂ±â0.5Â°C (both treatment and control) for the light period (14 h). Three biological replicates of the temperature treatments were grown under the same conditions. After 48 h of treatment, samples containing 45 grains with labels from the same region (middle to bottom part) of labelled ears were harvested, packed in aluminum foil, and flash-frozen in liquid nitrogen until further use. A total of 12 rice grain samples were harvested, i.e., controls (TC1, TC2 and TC3) and treatments (TT1, TT2 and TT3) of the three biological replicates of the heat-tolerant line, and controls (SC1, SC2 and SC3) and treatments (ST1, ST2 and ST3) of the three biological replicates of the heat-sensitive line.

2014-12-01 | E-MTAB-4348 | biostudies-arrayexpress

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Project description:RNA-seq analysis of cold-tolerant and cold-sensitive rice varieties at the seedling stage

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Oryza sativa

Project description:Comparative transcriptome analysis of different root types in rice under salinity stress

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Simple sequence repeat identification for RSS1 gene in multiple varieties of Oryza sativa

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

FL478 shotgun proteomic database of shoot and root of rice plants subjected to salinity stress

Project description:I'm a biochemist currently doing my PhD and the primary person involved in obtaining this data set. I'm currently working with rice at the in vitro level, greenhouse controlled conditions and field trials. I am studying the proteome of salinity tolerant varieties, the implication of gibberellins in height and tolerance to salinity, and finally biotechnology to reduce the time to obtain stable hybrid rice lines.

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Oryza sativa Japonica Group transcriptome sequencing

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.

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