3.3 Differentially expressed genes (DEGs) and differentially co-expressed genes (DCGs)
The DEGs between drought treatments vs control showed region-specific and treatment-difference (Fig. 4). The number of DEGs between heavy drought treatment vs control was greater than that between light drought treatment vs control (Fig. 4). In addition, the differentially co-expressed genes (DCGs) within these three regions were 19 (0.72%) between light drought treatment vs control (Fig. 4a), with 9 being up-regulated and 10 being down-regulated (Table S1); and was 845 (9.98%) between heavy drought treatment vs control (Fig. 4b), with 592 being up-regulated and 253 being down-regulated (Table S2). Therefore, in this study, we further analyzed the responses of individuals to heavy drought treatment based on DEGs and DCGs.
By KEGG functional enrichment analysis on DEGs, gene expressions were mainly enriched in the pathways of photosynthesis-antenna proteins (with 24 genes up-regulated), cyanoamino acid metabolism (with 13 genes up-regulated and 12 genes down-regulated) and photosynthesis (with 28 genes up-regulated and 1 genes down-regulated) for individuals from the eastern region (Fig. 5a; Table S3); enriched in the pathways of one carbon pool by folate (with 7 genes up-regulated and 2 genes down-regulated), cyanoamino acid metabolism (with 9 genes up-regulated and 5 genes down-regulated) and carbon fixation in photosynthetic organisms (with 27 genes up-regulated) for individuals from middle region (Fig. 5b; Table S4); and enriched in the pathways of flavonoid biosynthesis (with 7 genes up-regulated and 3 genes down-regulated), galactose metabolism (with 25 genes up-regulated and 7 genes down-regulated) and glycolysis / gluconeogenesis (with 39 genes up-regulated and 13 genes down-regulated) for individuals from the western region (Fig. 5c; Table S5). No significant pathway of DEGs between light drought treatment vs control was enriched in individuals from the middle and western regions.
By KEGG functional annotation analysis on 845 DCGs, biochemical metabolic pathways of the first category were identified: metabolism, genetic information processing, environmental information processing, cellular processes, and organismal systems. The pathways of second category were enriched, such as carbohydrate metabolism, amino acid metabolism, and lipid metabolism (Fig. 6). Among them, a large number of genes were enriched in the pathways whose descriptions were glycolysis / gluconeogenesis (with 18 genes up-regulated and 2 genes down-regulated), starch and sucrose metabolism (with 13 genes up-regulated and 3 genes down-regulated), MAPK signaling pathway - plant (with 7 genes up-regulated and 4 genes down-regulated) and plant hormone signal transduction (with 7 genes up-regulated and 3 genes down-regulated) (Table S6 & S7).