3.3.1. Flag-Leaf Specific Modules

Two specific flag-leaf modules with a contrasting pattern of expression were investigated in more detail for implications in the di fferential performance of the two genotypes under RDS. FL-M14 consisting of 140 genes (Table S10-1) had significantly higher expression profiles in all samples of the DTY-IL genotype under RDS, whereas a lower expression across the three other groups of samples was observed (Figure 4A). FL-M16 consisting of 102 genes (Table S10-2) had significantly lower expression in Swarna under RDS, whereas the three other groups of samples had a higher expression (Figure 4B).

FL-M14 enriched BP GO terms were "cellular amino acid biosynthetic process" as well as "cell wall organization or biogenesis" (Figure S12A). The enriched pathway included "biosynthesis of secondary metabolites", "fatty acid elongation", and "phagosome" while the overrepresented Interpro domains included "Expansin" as well as "Glycosyl transferase, family 43", and "Plant peroxidase" (Figure 5A). FL-M14 hub genes included amidase and expansin (Figure S13A; Table S11-1). Interestingly, numerous cell wall organization and biogenesis genes are upregulated in DTY-IL and downregulated in Swarna under RDS (Figure 6).

FL-M16 was enriched in "oxidation-reduction process" as well as "cellular carbohydrate metabolic process" (Figure S12B). The enriched pathways include "photosynthesis", "folate biosynthesis", and "vitamin B6 metabolism" while the overrepresented Interpro domains in FL-M16 included "Ferrodoxin—NAP reductase", "Multicopper oxidase", and "Photosystem antenna protein-like" (Figure 5B). FL-M16 hub genes included OsSub37—putative subtilisin homologue and cytochrome P450 (Figure S13B; Table S11-2).

**Figure 4.** Gene co-expression network analysis in flag-leaf under RDS. Bar plots of the module eigengene as representatives of gene expression profiles across samples in FL-M14 (module 14) (**A**) and FL-M16 (module 16) (**B**). *X*-axis represents 16 different samples across four different groups, while *Y*-axis corresponds to the eigengene value. Heatmaps showing gene expression levels of genes in FL-M14 and FL-M16. 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.

**Figure 5.** *Cont.*

**Figure 5.** Enrichment analysis of the functional categories in FL-M14 and FL-M16. Over-represented Interpro domains and enriched pathways in FL-M14 (**A**) and FL-M16 (**B**) in flag-leaf under RDS. Top significant pathways and Interpro domains are shown in *Y*-axis with the number of represented genes on the *X*-axis.

**Figure 6.** Cell wall organization and biogenesis during RDS in the flag-leaf tissue. Expression of cell wall organization or biogenesis related genes in drought-responsive modules between DTY-IL and Swarna are shown as log2 fold change heat-maps.
