Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16686926_1.fastq.gz | Fastqsanger.gz | |||
| SRR16686926_2.fastq.gz | Fastqsanger.gz | |||
| SRR16686927_1.fastq.gz | Fastqsanger.gz | |||
| SRR16686927_2.fastq.gz | Fastqsanger.gz | |||
| SRR16686928_1.fastq.gz | Fastqsanger.gz |
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Project description:Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. An auxin response factor, OsARF17, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17Hap1/HFR131Hap6 conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17–HFR131 interaction, and provided a potential breeding target for improvement of rice yield.
2023-03-17 | GSE224118 | GEO
Project description:Plant height is a major trait affecting yield potential in rice. Using a large-scale hybrid transcription factor approach, we identified the novel MYB-like transcription factor OsMPH1 (MYB-like gene of Plant Height 1), which is involved in the regulation of plant height in rice.Overexpression of OsMPH1 leads to increases of plant height and grain yield in rice, while knockdown of OsMPH1 leads to the opposite phenotypes. RNA-seq is used for exploring differences between OsMPH1 transgenic rice and wild-type plants.
2017-07-01 | E-MTAB-5759 | biostudies-arrayexpress
Project description:Polyploidization is one of the effective ways to improve plant height and yield of rice (Oryza sativa L.). However, the molecular mechanism of regulation is not yet fully understood. Here, we investigated the agronomic traits of diploid (Balilla-2x) and tetraploid (Balilla-4x) of japonica rice variety Balilla. Compared with Balilla-2x, Balilla-4x exhibited significantly increased plant height, spike length and yield per plant. RNA-seq analysis of the leaves of Balilla-2x and Balilla-4x was performed and the results showed that the expression levels of yield related genes (e.g., STH1, OsYUC9, and OsDEP1) were significantly upregulated in Balilla-4x rice plants, these genes are related to plant height and panicle development. These results indicated that polyploidization changed the expression of genes related to agronomic traits such as plant height and spike length, thereby increasing rice yield. This study provides a further basis for understanding the yield of rice after polyploidization, and can serve as a new theoretical reference for breeding high-yielding rice varieties achieved.
2024-01-30 | GSE254291 | GEO
Project description:Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2).
2012-02-12 | GSE35729 | GEO
Project description:Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2). Leaf tissues of 6-week-old LRK1 060615 transgenic rice and control 9311 rice (10 plants each) were selected.
2012-02-12 | E-GEOD-35729 | biostudies-arrayexpress
Project description:Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the profile of the binding peaks of OsGRF7 with GFP antibody in 35S:GRF7-GFP overexpression lines.
2020-04-19 | GSE109800 | GEO
Project description:Rice genome contains three genes that encode for glutathione reductase (GR) viz., OsGR1, 2 and 3. GR is an important component of the anti-oxidative machinery of plant cells. GR2 down-regulated plants were produced by RNAi mediated down-regulation of GR2 (GR2-Ri). GR2-Ri plants were significantly smaller /reduced plant height compared to WT(Wild type), under control conditions. Microarray analysis was carried out to identify the genes which are differentially regulated in GR2-Ri compared to WT, respectively, under control conditions.
2024-08-30 | E-MTAB-7171 | biostudies-arrayexpress
Project description:Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the differential expressed genes between GRF7OE and WT plants.
2020-04-19 | GSE109801 | GEO
Project description:By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele.
2012-04-01 | GSE35762 | GEO