3.3.2. Panicle Specific Modules

Two contrasting panicle modules (P-M10 and P-M15) were investigated in more detail. P-M10 consisting of 138 genes (Table S12-1) and P-M15 consisting of 73 genes (Table S12-2) had significant interaction with drought response in a genotype-specific manner. P-M10 had significantly higher expression profiles in all samples of DTY-IL under RDS and a lower expression pattern across the other three groups of samples (Figure 7A). P-M15 had significantly lower expression profiles in all samples in Swarna under RDS, whereas the three other groups of samples had a higher expression (Figure 7B).

**Figure 7.** Gene co-expression network analysis in panicle under RDS. Bar plot of the module eigengene as representatives of the gene expression profiles across different samples in P-M10 (module 10) (**A**) and P-M15 (module 15) (**B**). *X*-axis represents 15 different samples across four different groups, while *Y*-axis corresponds to the eigengene value. Heatmaps showing gene expression levels of genes in P-M10 and P-M15. Columns represent samples, while rows correspond to genes in the module. Red indicates positive and blue negative expression profile. S.C = Swarna control, S.D = Swarna under RDS, IL.C = DTY-IL control, IL.D = DTY-IL under RDS.

P-M10 enriched BP GO terms were "calcium ion transmembrane" as well as "lipid biosynthetic process" (Figure S14A). Pathway enrichment analysis included "glutathione metabolism", "phenylpropanoid biosynthesis", and "ribosome" while the overrepresented Interpro domains were "Protein kinase" as well as "Plant peroxidase" (Figure 8A). P-M10 hub genes included OsWAK receptor-like cytoplasmic kinase and a serine-type peptidase (Figure S15A; Table S13-1). Analysis of genome-scale metabolic pathways in the DTY-IL revealed the up-regulation of genes involved in the biosynthesis of antioxidant enzymes and metabolites (Figure 9 and Figure S14).

**Figure 8.** Enrichment analysis of the functional categories in P-M10 and P-M15. Over-represented Interpro domains and enriched pathways in P-M10 (**A**) and P-M15 (**B**) in panicle under RDS. Top significant pathways and Interpro domains are shown in *Y*-axis with the number of represented genes on the *X*-axis.

**Figure 9.** Regulation of metabolic pathways during RDS in panicle. The metabolic pathways enriched in the drought-responsive modules P-M10 (M10) and P-M15 (M15) between DTY-IL and Swarna under RDS are shown in heat-maps representing their expression profile. The scale represents a log2 fold change in expression. IL = DTY-IL.

P-M15 were GO enriched for "carboxylic acid metabolic process" as well as "coenzyme metabolic process" (Figure S14B). The enriched pathways includes "carbon metabolism", "glutathione metabolism", and "pentose phospate pathway" while the overrepresented Interpro domains included "Cysteine synthase" and "Thiolase-like, subgroup" (Figure 8B). P-M15 hub genes included the glycosyl hydrolase family 29, and dehydrogenase/reductase (Figure S15B; Table S13-2).

The consensus network from the flag-leaf and panicle transcriptomes contained few significant overlaps in module classifications between the flag-leaf and panicle networks, consistent with the tissue-specific expression under RDS [23] (Figure S16). Similarly, colored modules between the flag-leaf and panicle networks contained a few significant overlaps of genes with a common consensus network module, consistent with their similar eigengenes profiles (Figures S10 and S11). The significant overlap portrays a common expression pattern for each condition of both genotypes (FL-M1 and P-M1, and FL-M2 and P-M2) and a common expression pattern for each genotype on both conditions (FL-M6 and FL-M7, and P-M5 and P-M6) in the flag-leaf and panicle networks, respectively.
