Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions
- New York University, United States
- International Rice Research Institute, Philippines
- Simons Center for Data Analysis, Simons Foundation, United States
Figures
Figure 1
Modeling environmental and developmental effects on rice gene expression in the field.
(A) Experimental design: fifteen sampling timepoints for each of the 16 season/field/replicate/genotype series amounts to 240 samples, representative of 30 different sets of climatic conditions, …
Figure 2
In the dry season analysis, expression patterns of the two genotypes are highly correlated for most clusters while for the few other clusters, differences between the genotypes are poorly explained by the models (high model MSEs for clusters with low correlation).
(A) Model MSE vs. correlation (Pearson coefficient) between the genotypes for the 56 dry season cluster means. (B) Model MSE vs. correlation between the fields for the 56 dry season cluster means. MS…
Figure 3
Cluster 9 of the two-season analysis: its environmental/developmental model and some of the genes it contains that have a potential function in environmental response.
(A) Gene expression for the cluster mean (grey) and spread (calculated as 10% and 90% quantile of all genes in the cluster for each data point; grey area), and cluster model (red). (B) Scaled …
Figure 4
Classification of the 53 clusters from the two-season analysis based on field correlation in the dry and wet seasons.
Each dot represents a cluster with the size of the dot proportional to the number of genes in the cluster. The 27-gene clusters with igh genotype correlation (r > 0.9, Pearson coefficient) are …
Figure 5
Summary of the ED models selected for the 27-gene clusters with high genotype correlation in the two-season analysis.
(A) Justification for the grouping of model parameters: heat-map of the correlation between the ED parameters selected at least once in the models. For some parameters that have strong negative …
Figure 6
Co-expression and variance of genes involved in environmental response.
High variance is represented with lighter shades of gray. The genes represented have a genotype correlation above 0.8. Gene names starting with “Os” are rice gene names, others are the names of A. …
Figure 7
Transferability of two seasons irrigated field models to an independent dataset of rice gene expression under temperate climate.
Models were selected for 60 clusters using our expression data in the irrigated field during the wet and dry seasons. The parameters from these models that could be transferred to explain the mean …
Tables
Table 1
Climatic parameters for the environmental/developmental models and their abbreviations. Parameters calculated from the weather data are mostly ordinary averages (linear: L) for a large range of time …
| Average/change for the last | Temperature (tp) | Relative humidity (hu) | Solar radiation (so) | Wind speed (wd) | Atmospheric pressure (ps) | Rainfall (ra) | |
|---|---|---|---|---|---|---|---|
| Sampling time | 15 min (15 min) | L | L | L NL− NL+ | L | L | L |
| Short-term averages | 1 hr (1 hr) | L | L | L NL− NL+ | L | L | L |
| 4 hr (4 hr) | L | L | L NL− NL+ | L | L | L | |
| 24 hr (24 hr) | L | L | L | L | L | L | |
| Long-term averages | 3 d (3 d) | L | L | L | L | L | L |
| 6 d (6 d) | L | L | L | L | L | L | |
| 10 d (10 d) | L | L | L | L | L | L | |
| 15 d (15 d) | L | L | L | L | L | L | |
| Recent change | 20 min (δ20 min) | D | D | D | D | ||
| 1 hr (δ1 hr) | D | D | D | D | |||
| 2 hr (δ2 hr) | D | D | D | D | |||
| Fluctuations | 1 hr (ε1 hr) | R | |||||
| 4 hr (ε4 hr) | R | ||||||
| 24 hr (ε24 hr) | R |
Additional files
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Supplementary file 1
Detailed characteristics and models for all the clusters in the two-season analysis; results used for the comparison of the partial Nagano dataset with our analysis.
- https://doi.org/10.7554/eLife.08411.011
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Supplementary file 2
Weather data for the dry and wet season experiments.
- https://doi.org/10.7554/eLife.08411.012
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Source code 1
Clustering, model selection for the two-season analysis and analysis of the partial Nagano dataset.
- https://doi.org/10.7554/eLife.08411.013
