Clustering of Coexpressed Genes in the JA Gene Regulatory Network and Identification of Novel Components of JA-Dependent Resistance.

(A) The set of 3611 genes showing differential expression in Arabidopsis leaves following exogenous application of MeJA was partitioned into 27 distinct coexpressed gene clusters using SplineCluster. The heat map shows the mean gene expression profile for each cluster, with red and blue indicating upregulation and downregulation of expression (log₂-fold change [MeJA/mock]), respectively.

(B) Significantly overrepresented TF families within clusters of genes upregulated (clusters 1-14; red) or downregulated (clusters 15–27; blue) in response to MeJA treatment (hypergeometric test; P ≤ 0.001).

(C) Quantification of disease symptoms of wild-type Col-0, highly susceptible ERF TF mutant ora59, and T-DNA insertion lines for selected genes ERF16, MYB59, and bHLH27 (members of coexpression clusters 2, 4, and 1, respectively) at 3 d after inoculation with B. cinerea. Disease severity of inoculated leaves was scored in four classes ranging from restricted lesion (class I), nonspreading lesion (class II), spreading lesion (class III), up to severely spreading lesion (class IV). The percentage of leaves in each class was calculated per plant (n  > 20). Asterisk indicates statistically significant difference from Col-0 (χ² test; P ≤ 0.05).

(D) Performance of M. brassicae larvae on Col-0, highly susceptible triple bHLH TF mutant myc2,3,4, and T-DNA insertion lines for selected genes ANAC056 (coexpression cluster 13) and bHLH27. The larval fresh weight was determined after 8 d of feeding. Asterisk indicates statistically significant difference from Col-0 (two-tailed Student's t test for pairwise comparisons; P ≤ 0.05; n = 30; error bars are se).

(E) Quantification of disease symptoms of Col-0, myb48, myb59, myb48 myb59, and ora59 mutant lines at 3 d after inoculation with B. cinerea. Disease severity of inoculated leaves was scored as described in (C) (n  > 20). Asterisk indicates statistically significant difference from Col-0 (χ² test; P ≤ 0.05).

(F) Performance of M. brassicae larvae on Col-0 and myb48, myb59, and myb48 myb59 mutant lines. The larval fresh weight was determined after 12 d of feeding. Asterisk indicates statistically significant difference from Col-0 (two-tailed Student's t test for pairwise comparisons; P ≤ 0.05; n = 30; error bars are se).

(G) Heat map indicating hypergeometric enrichment P value of genes differentially expressed in myb48 myb59 (compared with Col-0) in each MeJA-induced coexpression cluster.