Fig 1.
Number of DEGs between oscoi lines and WT plants.
a. Number of DEGs identified in crown root tips from oscoi1ab and oscoi2 lines compared to WT plants. b. Venn diagrams showing specific and common DEGs found in oscoi1ab and oscoi2 lines compared to WT plants.
Fig 2.
Number of DEGs in response to JA treatment in WT plants and oscoi lines.
a. Number of DEGs in crown root tips after 6h JA treatment (5 μM). b. Venn diagrams showing specific and common DEGs in WT plants and oscoi lines in response to JA. Up: up-regulated genes, down: down-regulated genes.
Fig 3.
Expression of JA-related genes in response to JA treatment in WT plants and in oscoi mutants.
a. Expression pattern of genes related to JA metabolism and perception b. Venn diagrams showing specific and common DEGs encoding for transcription factors (Up: up-regulated genes, down: down-regulated genes). c. Expression pattern of genes related to plant defense. For heatmaps, the key color represents the log2FC values of the DEGs identified between JA-treated samples and controls samples (see S6 Table for detailed values).
Fig 4.
Mapman analysis of the DEGs identified in WT plants and oscoi lines in response to JA.
a. Mapman metabolism overview. b. Mapman representation of genes associated to secondary metabolism pathways. The key color represents the log2FC values between JA-treated samples and controls samples.
Fig 5.
Metabolic pathways controlled by OsCOI2 in response to JA treatment.
a. Expression pattern of genes related to cell expansion. b. Expression pattern of genes related to photosynthesis. c. Expression pattern of genes related to the phenylpropanoid pathway (PPP), including the shikimate pathway and the synthesis of phenylalanine, the PPP precursor. The key color represents the log2FC values of the DEGs identified between JA-treated samples and controls samples (see S6 Table for detailed values).
Fig 6.
OsCOI2-dependent expression of Diterpene Phytoalexins (DP) biosynthesis genes.
a. Expression pattern of genes related to the methylerythritol phosphate pathway (MEP), the known TFs involved in DP genes regulation, and DP biosynthesis genes located on the c2BGC (chromosome 2 biosynthesis gene cluster), on the c4BGC (chromosome 4 biosynthesis gene cluster) and on DGC7: (diterpenoid gene cluster on chromosome 7). The key color represents the log2FC values of DEGs between JA-treated samples and controls samples (see S6 Table for detailed values). c. Schematic representation of DP biosynthesis. Oryzalexin S biosynthesis was recently elucidated [23].
Fig 7.
Metabolite accumulation in rice roots submitted to JA treatment.
The key color represents the Log2FC values between JA-treated samples and controls samples. Stars indicate significant difference levels between JA-treated samples and controls samples (p < 0.01) (see S9 Table for detailed values).
Fig 8.
Phytoalexins accumulation in rice roots submitted to JA treatment.
Phytoalexin levels in rice roots from control plants (C) and from plants submitted to a 24h JA treatment (5 μM). In the boxplots, whiskers denote minimum/maximum values, the box defines the interquartile range and the center line represents the median. Asterisks above the boxplots indicate significant differences between treated and control plants. Asterisks above the brackets indicate significant differences between lines and WT plants (One way-ANOVA with Tuckey’s multiple comparisons test, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001).