Uniformed Viewer for Integrative Omics

Overview: Rice Hormonome-Transcriptome

1. Introduction

Plant hormones play an important role as signaling molecules in the regulation of growth and development by controlling the expression of downstream target genes. Furthermore, hormone signaling is a complex network involving interaction of and regulation by other phytohormones. Thus, a comprehensive and integrative analysis of hormone and gene expression will contribute to the understanding of the overall mechanism of action of plant hormones. This database provides an integrated data set of hormonome and transcriptome analyses in 14 organs of the rice plant at the reproductive stage and in gibberellin-related mutants. Users can easily search objective data by using plant hormone names, probe IDs, locus IDs, and gene descriptions as queries. The data of transcripts and hormones are easily visualized as heat maps.

2. Materials and Methods

2-1. Rice plant organs

Oryza sativa L. cv. Nipponbare was grown in soil in a greenhouse with irrigation and supplemental artificial light. At the heading stage, the plant organs shown in Table 1 were harvested and immediately frozen in liquid nitrogen after measurement of fresh weight. The harvested tissues were stored at -80°C until extraction of phytohormones or total RNA.

2-2. GA mutants

Growth and harvest conditions of GA mutants (Table 1) were described in a previous paper (Kojima et al. 2009).

Table 1. Rice plant organs used in hormone and transcriptome analyses
Numbers (Nos.) correspond to the numbers shown in Figure 1.
Nos. Plant organs Abbreviations Biological replicate
GeneChip Hormone
Organs at the heading stage
1Flowers before anthesisFlw33
2Panicle branchesPBr33
3Top part of internode IInN I-top33
4Basal part of internode IInN I-bsl33
5Node INod I33
6Node IINod II33
7Tip of the blade of the flag leaf FLB-tip33
8Middle part of the blade of the flag leafFLB-mid33
9Basal part of the blade of the flag leafFLB-bsl33
10Top part of the sheath of the flag leafFLS-top33
11Basal part of the sheath of the flag leafFLS-bsl23
12Whole blade of the flag leafFLB13
13Whole blade of leaf 2 counted down from the flag leafLB-213
14Whole blade of leaf 4 counted down from the flag leafLB-413
Gibberellin-related mutants
Shoot of Taichung 65 (control)T6533
Shoot of gid1-3 mutantgid133
Shoot of gid2-1 mutantgid233
Shoot of slr1 mutantsir133

2-3. Phytohormone analysis

Phytohormone extraction, purification, and quantification were carried out as described previously (Kojima et al. 2009).

Table 2. Plant hormones and related compounds analyzed in this study.
Hormone Class Abbreviation Physiological property
Abscisic acid Abscisic acid ABA Active compound
Indole-3-acetic acid Auxin IAA Active compound
Indole-3-acetyl-L-alanine Auxin IAAla Deactivated compound
Indole-3-acetyl-L-isoleucine Auxin IAIle Deactivated compound
Indole-3-acetyl-L-leucine Auxin IALeu Deactivated compound
Indole-3-acetyl-L-aspartic acid Auxin IAAsp Deactivated compound
Indole-3-acetyl-L-tryptophan Auxin IATrp Deactivated compound
Indole-3-acetyl-L-phenylalanine Auxin IAPhe Deactivated compound
N6-(Δ2-Isopentenyl)adenine Cytokinin iP Active compound
N6-(Δ2-Isopentenyl)adenine riboside Cytokinin iPR Intermediate
N6-(Δ2-Isopentenyl)adenine ribotides Cytokinin iPRPs Intermediate
N6-(Δ2-Isopentenyl)adenine-N7-glucoside Cytokinin iP7G Deactivated compound
N6-(Δ2-Isopentenyl)adenine-N9-glucoside Cytokinin iP9G Deactivated compound
trans-Zeatin Cytokinin tZ Active compound
trans-Zeatin riboside Cytokinin tZR Intermediate
trans-Zeatin ribotides Cytokinin tZRPs Intermediate
trans-Zeatin-N7-glucoside Cytokinin tZ7G Deactivated compound
trans-Zeatin-N9-glucoside Cytokinin tZ9G Deactivated compound
trans-Zeatin-O-glucoside Cytokinin tZOG Deactivated compound
trans-Zeatin riboside-O-glucoside Cytokinin tZROG Deactivated compound
trans-Zeatin ribotide-O-glucosides Cytokinin tZRPsOG Deactivated compound
cis-Zeatin Cytokinin cZ Active compound
cis-Zeatin riboside Cytokinin cZR Intermediate
cis-Zeatin ribotides Cytokinin cZRPs Intermediate
cis-Zeatin-O-glucoside Cytokinin cZOG Deactivated compound
cis-Zeatin riboside-O-glucoside Cytokinin cZROG Deactivated compound
cis-Zeatin ribotide-O-glucosides Cytokinin cZRPsOG Deactivated compound
Dihydro-zeatin Cytokinin DZ Active compound
Dihydro-zeatin riboside Cytokinin DZR Intermediate
Dihydro-zeatin ribotides Cytokinin DZRPs Intermediate
Dihydro-zeatin-N9-glucoside Cytokinin DZ9G Deactivated compound
Gibberellin A1 Gibberellin GA1 Active compound
Gibberellin A3 Gibberellin GA3 Active compound
Gibberellin A4 Gibberellin GA4 Active compound
Gibberellin A7 Gibberellin GA7 Intermediate
Gibberellin A8 Gibberellin GA8 Deactivated compound
Gibberellin A9 Gibberellin GA9 Intermediate
Gibberellin A12 Gibberellin GA12 Intermediate
Gibberellin A19 Gibberellin GA19 Intermediate
Gibberellin A20 Gibberellin GA20 Intermediate
Gibberellin A24 Gibberellin GA24 Intermediate
Gibberellin A44 Gibberellin GA44 Intermediate
Gibberellin A53 Gibberellin GA53 Intermediate

2-4. Transcriptomic analysis

Microarray analysis was performed using a GeneChip® Rice Genome Array (Affymetrix). Extraction of total RNA was carried out by using RNeasy® Mini Kit (QIAGEN). Preparation of labeled target cRNA and the subsequent purification and fragmentation of cRNA were carried out using Genechip® One-Cycle Target Labeling and Control Reagents (Affymetrix). Double-stranded cDNA was prepared from 5 µg of total RNA. Hybridization, washing, staining, and scanning were performed as described in the supplier’s protocol. A 5-µg aliquot of fragmented cRNA was used for hybridization to microarrays. These experiments were conducted according to the manufacturer's guidelines.

Figure 1. Illustration of rice plant organs used for hormone and transcriptome analyses. 1, Flowers before anthesis; 2, Panicle branches; 3, Top part of internode I; 4, Basal part of internode I; 5, Node I; 6, Node II; 7, Tip of the blade of the flag leaf; 8, Middle part of the blade of the flag leaf; 9, Basal part of the blade of the flag leaf; 10, Top part of the sheath of the flag leaf; 11, Basal part of the sheath of the flag leaf; 12, Whole blade of the flag leaf; 13, Whole blade of leaf 2 counted down from the flag leaf; 14, Whole blade of leaf 4 counted down from the flag leaf. The numbers correspond to the numbers shown in Table 1.

3. References

4. Raw Data

4-1. Phytohormone analysis

4-2. Transcriptomic analysis

5. Contact Person

Plant Productivity Systems Research Group,
Plant Science Center, RIKEN