Ontology highlight
ABSTRACT:
PROVIDER: PRJNA855573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19976200_1.fastq.gz | Fastqsanger.gz | |||
| SRR19976200_2.fastq.gz | Fastqsanger.gz | |||
| SRR19976201_1.fastq.gz | Fastqsanger.gz | |||
| SRR19976201_2.fastq.gz | Fastqsanger.gz | |||
| SRR19976202_1.fastq.gz | Fastqsanger.gz |
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Project description:Genetic improvement of rice for enhanced input use efficiency
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Project description:Genetic improvement of rice for enhanced input use efficiency
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Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.
2010-12-23 | GSE26280 | GEO
Project description:Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChip® Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97.
2012-01-01 | GSE32426 | GEO
Project description:Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.
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Project description:The biological functions of differently expressed proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (-20 kPa or -40 kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower expressions of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (-20 kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice.
2015-08-05 | PXD001046 | Pride
Project description:Improvement of phosphorus (P) uptake by crops is a prerequisite for sustainable agriculture. Rice (Oryza sativa L.) PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) increases root growth and total P uptake. Here, a biogeographic survey of rice demonstrates OsPSTOL1 loss in a subset of japonica rice after the temperate-tropical split and frequent absence in paddy varieties of east Asia. OsPSTOL1 absence or loss-of-function alleles prevail in landraces from regions with fertilizer use and controlled irrigation, suggesting it is an adaptive genetic variant in low nutrient rainfed ecosystems. OsPSTOL1 is a truncated member of a family of multi-module kinases associated with microbial interactions. We demonstrate that ectopic expression of OsPSTOL1 in wheat (Triticum aestivum L.) increases shoot and root growth under low P conditions, promotes root plasticity, and hastens induction of the low P response pathway. OsPSTOL1’s influence on adaptive root development in wheat validates its potential for broad utilization in crop improvement.
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Project description:Rice (Oryza sativa), the major staple food crop is being cultivated under varying ecosystems ranging from irrigated lowland to rainfed upland environments. Improvement in the rice production under drought prone unfavourable environment depends on the development of drought tolerant genotypes which needs thorough understanding of physiological and molecular events behind the tolerance mechanism. There is considerable genetic variation for drought tolerance mechanism within the cultivated gene pool. To understand the diversity of drought response, two indica rice genotypes namely, i) Apo, an up-land drought tolerant indica veriety from Philippines and ii) IR64, a popular high yielding drought susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under control and drought stressed conditions during vegetative phase. Keywords: Drought response
2012-05-01 | GSE5978 | GEO
Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.
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