Expression data for reproductive development in rice
Sanjay Kapoor, University of Delhi
Project Accession:
IADA-PRqgvszrus
Project Description:
Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development.
Project Mode:
Individual
Access Mode:
Open Access
Grant No.:
NA
Funding Agency:
DBT and CSIR
Release Date:
Sept. 17, 2026
Organism Category:
Plant
Number of Study:
1
Study(s):
Study Date:
Sept. 18, 2026
Study Type:
Gene Expression Profiling (EFO:0002770)
Study Abstract:
Plants undergo two major phases of development: vegetative and reproductive. During the vegetative phase, the shoot apical meristem (SAM) gives rise to leaves, while the root apical meristem produces roots. As development progresses, the SAM undergoes a transition from vegetative to reproductive growth, a process known as floral transition, which ultimately leads to the formation of flowers and seeds. Over the past decade, significant advances have been made in understanding the molecular and genetic mechanisms regulating reproductive development in plants, largely through studies conducted in Arabidopsis thaliana. In the present study, we investigated the spatial and temporal patterns of gene expression across different tissues, organs, and developmental stages of rice using microarray technology. This approach enabled us to identify genes that are differentially expressed during different stages of reproductive development and provided insights into the molecular processes associated with rice reproduction.
Organism:
Oryza sativa (Taxon ID: 4530)
Authors:
- Mukesh Jain, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, mjain@jnu.ac.in
- Pinky Agarwal, BRIC-National Institute of Plant Genome Research, pinky.agarwal@nipgr.ac.in
- Sanjay Kapoor, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, kapoors@genomeindia.org
- Akhilesh K. Tyagi, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, akhilesh@genomeindia.org
- Jitendra P Khurana, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, khuranaj@genomeindia.org
- Swatismita Ray, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, swatismita.ray@south.du.ac.in
- Aashima Nijhawan, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, aashima_nijhawan@yahoo.com
- Rita Arora, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India, rita.arora@south.du.ac.in
Publications:
10.1104/pp.106.091900
Keywords:
Rice (Oryza sativa), Microarray array, reproductive development, developmental stages, gene expression
Samples:
45 Download
Experiment(s):
Experiment Description:
Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.
Experiment Date:
Jan. 24, 2006 - July 1, 2006
Experiment Technology:
RNA Microarray (OBI:0000632)
Experiment Type:
Expression profiling by array
Molecule Name:
RNA
Instrument Model:
Affymetrix Rice Genome Array
Experiment Label:
Biotin
Experiment Protocols:
- Growth Protocol - Rice seeds were disinfected with 0.1% HgCl2 for 1 h, thoroughly washed with RO (reverse-osmosis) water and soaked overnight in RO water. Seedlings were grown in RO water, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark.
- Normalization Data Transformation Protocol - The data were analyzed with GeneChip Operating Software (GCOS 1.2.1) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was arbitrarily set to 100.
- Array Scanning and Feature Extraction Protocol - GeneChips were scanned using GeneChip Scanner 3000.
- Nucleic Acid Extraction Protocol - Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions
- Nucleic Acid Hybridization to Array Protocol - Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v5.
- Nucleic Acid Labeling Protocol - Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
- Sample Collection Protocol - Different developmental stages of rice panicle were obtained from field-grown rice (Oryza sativa ssp. indica var. IR64). Young panicles were taken out from the sheath and measured to be categorized into six groups (P1, 0-3 cm; P2, 3-5 cm; P3, 5-10 cm; P4, 10-15 cm; P5, 15-22 cm; P6, 22-30 cm) based on panicle length and landmark developmental events (Itoh et al., 2005), and frozen in liquid nitrogen. Rice seeds were tagged from the day of pollination (0 DAP) and collected on each DAP from 0 to 30 DAP; these were pooled into S1 (0-2 DAP), S2 (3-4 DAP), S3 (5-10 DAP), S4 (11-20 DAP) and S5 (21-29 DAP). Mature leaves were harvested from the same plants. Roots were harvested from 7-day-old light-grown seedlings grown hydroponically in RO (reverse-osmosis) water.
Experiment Design:
Development or Differential Design, Time Series Design
Datafiles:
Raw Files: 45