Oryza sativa Japonica Group
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ABSTRACT:
PROVIDER: PRJNA143833 | ENA |
REPOSITORIES: ENA
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Project description:The root system is a crucial determinant of plant growth potential because of its important functions, e.g., acquisition of water and nutrients, structural support, and interaction with symbiotic organisms. Elucidating the molecular mechanisms of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants including rice. As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray analysis approach. We performed comprehensive microarray analysis of a rice crown root using laser microdissection and collected a total of 13 samples (3 replicates for each sample except for one sample, 38 total microarray data) representing 8 different developmental stages along the longitudinal axis and 3 distinct tissue-types along the radial axis at 2 different developmental stages. The 8 developmental stages represent root cap, division zone, elongation zone and maturation zone_I, II, III, IV and V. The 3 tissue-types represent epidermis/exodermis/sclerenchyma, cortex, and endodermis/pericycle/stele. In the maturation zone_V, the cortex consisted largely of aerenchyma (non-living cells) and was not used for the microarray analysis.
2011-10-25 | E-GEOD-30136 | 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:Developmental and functional responses of rice root system to soil water and nutrient conditions
| PRJDB4462 | ENA
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE We constructed nine SAGE libraries parallelly, including root at the first tillering stage, leaf at the milky stage of rice grain maturation, and panicle at the pollen-maturing stage of hybrid rice (LYP9) and its paternal lines (9311, PA64s).
2007-06-07 | E-GEOD-8048 | biostudies-arrayexpress
Project description:Transcriptome profiling of various organs at different developmental stages in rice (paired-end)
| PRJNA243368 | ENA
Project description:Transcriptome profiling of various organs at different developmental stages in rice (single-end)
| PRJNA243371 | ENA
Project description:Rice has a fibrous root system with a primary root, lateral roots and crown roots. The cellular origins and early morphologies of the three root types vary greatly, but the adult structures are remarkably similar. Previous studies have highlighted diverse mechanisms involved in rice roots formation However, the gene expression reprograming and the underling epigenetic mechanisms of cell differentiation and initiation of the different roots are not studied. Here, we analyzed spatiotemporally resolved transcriptomes and DNA methylomes during the initiation processes of the three root types using a precise laser microdissection (LM) coupled with RNA-Seq and BS-seq. The analysis reveals distinct gene expression programs during the first stages during the initiation of the three root types. DNA methylome analysis uncovers a dynamic but distinct CHH methylation reprogramming during initiation of the three roots, with a genome-wide decrease of CHH methylation in crown and lateral root initials, but an increase in embryonic root primordium. In addition, a more drastic reprogramming of CHH methylation was observed in lateral root initials. Together, the results provide stage-specific gene expression signatures of the rice roots initiation and show distinct epigenetic and gene expression reprograming during the formation of the three different root types in rice.
2020-02-01 | GSE136767 | GEO
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE
2007-06-08 | GSE8048 | GEO
Project description:Differentially expressed genes from different developmantal stages in rice
| PRJNA99403 | ENA
Project description:Plant root transcriptome profiling of Azospirillum-rice cooperation
| PRJNA254488 | ENA