Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles

ABSTRACT: Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles

PROVIDER: PRJNA634492 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11830100.fastq.gz	Fastqsanger.gz
	SRR11830101.fastq.gz	Fastqsanger.gz
	SRR11830102.fastq.gz	Fastqsanger.gz
	SRR11830103.fastq.gz	Fastqsanger.gz
	SRR11830104.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles

Project description:Purpose: To confirm the effects of Prl5 and Pbl6 (APO1) on panicle length at the gene expression level, we performed RNA-seq analysis to compare the expression patterns of these genes in young panicles of the near isogenic lines (NILs). Results: Gene Ontology (GO) representation analysis indicated that the biological functions of the two genes are quite different. Conclusions: RNA-seq analysis revealed that these two genes independently regulate panicle length at the level of gene expression.

2020-05-23 | GSE151043 | GEO

Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles.

Project description:Panicle architecture directly affects crop productivity and is a key target of high-yield rice breeding. Panicle length strongly affects panicle architecture, but the underlying regulatory mechanisms are largely unknown. Here, we show that two quantitative trait loci (QTLs), PANICLE RACHIS LENGTH5 (Prl5) and PRIMARY BRANCH LENGTH6 (Pbl6), independently regulate panicle length in rice. Prl5 encodes a gibberellin biosynthesis enzyme, OsGA20ox4. The expression of Prl5 was higher in young panicles resulting in panicle rachis elongation. Pbl6 is identical to ABERRANT PANICLE ORGANIZATION 1 (APO1), encoding an F-box-containing protein. We found a novel function that higher expression of Pbl6 is responsible for primary branch elongation. RNA-seq analysis revealed that these two genes independently regulate panicle length at the level of gene expression. QTL pyramiding of both genes increased panicle length and productivity. By combining these two genes in various combinations, we designed numerous panicle architecture without trade-off relationship.

| S-EPMC7289860 | biostudies-literature

bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage

Project description:Whole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage The aim of this study was to identify candidate genes responsible for grain number per panicle by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 20 differentially expressed genes, respectively. The differentially expressed genes were shorted to 4 on the basis of their occurance in the QTL region (responcible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.

2010-01-01 | GSE17169 | GEO

ABERRANT PANICLE ORGANIZATION2 controls multiple steps in panicle formation through common direct-target genes

Project description:At the transition from vegetative to reproductive growth in rice, a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem (SAM) to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor. APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites by ChIP-seq analysis. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation at the reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.

2024-04-09 | GSE263431 | GEO

bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage

2009-12-31 | E-GEOD-17169 | biostudies-arrayexpress

Microarray using WT (Dongjin rice) and OsBUL1KO Panicle samples

Project description:We compared transcripts using microarray hybridization between panicle samples of WT and OsBUL1 KO.

2017-09-05 | GSE93715 | GEO

New HLA alleles

Project description:New HLA alleles

| PRJEB29858 | ENA

Dynamic profile of gene expression in rice panicle under high temperature

Project description:To comprehend the profile of rice gene expression at reproductive stage under high temperature, Agilent 4M-CM-^W44k rice oligo microarray experiments were carried out using rice panicle of developmental stage 7-9 at 0min, 20min, 1hr, 2hr, 4hr, and 8hr after the treatment of 40 degree centigrade, and the significantly expressed genes mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response were identified. Among them, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat. The results of motif co-occurrence on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3, and unraveled the possible cross-talk mechanism during heating. The response model central to ROS combined with transcriptome data indicated the great importance to maintain ROS balance in heat response in rice panicle and the wide existing of cross-talks. Heat shock induced gene expression in rice panicle of developmental stage 7-9 was measured at 0min, 20min, 1hr, 2hr, 4hr, and 8hr after the treatment of 40 degree centigrade in plant growth chamber. Two independent replicate experiments were performed at each time point.

2012-11-28 | E-GEOD-38665 | biostudies-arrayexpress

Down-regulated expression of OsDCL3b affects small RNA biogenesis and panicle development in rice

Project description:Two types of small (18-24 nt) non-coding RNAs (ncRNAs), microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been found to exist widely in higher plants. OsDCL3b has just been reported to process the 24-nt phased small RNAs in rice, which are preferentially expressed in panicle. In this study, we find that down-regulated expression of OsDCL3b leads to lower pollen sterility and seed setting rate, which results in decreased grain yield per plant in rice. Next, small RNA and mRNA sequencing were performed to study the decrease of pollen fertility and seed setting rate. 942 differentially expressed genes were identified, and some of them have already been known to be involved in rice panicle development. Our results indicate that there is a close correlation between small RNA and rice yield.

2019-04-12 | GSE102747 | GEO

The drought-responsive gene expression in rice panicle

Project description:The young panicles 2 cm length were used for expression analysis in well watered control and drought stressed treatment. The panicle samples from biological replicates of six rice varieties were obtained in three independent experiments. The expression profiles were generated using Affymetrix rice genome arrays.

2017-06-14 | GSE83378 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data