## 3 Results
### Expression of IAA and Cytokin Hormone Metabolism and Signaling Genes  
Auxin (IAA) and cytokinin are also important phytohormes that regulate many aspects of plant growth and development. Plants possess two major pathways for IAA hormone metabolism: the tryptophan (Trp)-independent and Trp-dependent pathways. The Trp-dependent pathway contains several routes: IAM, IPA, TAM, and IAOX [30; 31]. In our dataset, there was a total of 64 metabolites and signaling unigenes of IAA and cytokinin (Tables S11 and S12). For IAA hormone metabolism, 36 unigenes representing IAA metabolic enzymes, including anthranilate synthase (ASA), phosphoribosylanthranilate transferase (PAT), phosphoribosylanthranilate isomerase (PAI), indole-3-glycerol phosphate synthase (IGS), tryptophan synthase \(\alpha\) (TSA), tryptophan synthase \(\beta\) (TSB), amidase1 (AMI1) for the indole-3-acetamide (IAM) route, aldehyde oxidase (AAO), and flavin monooxygenase (YUC) for the indole-3-pyruvate acid (IPA) route, and cytochrome P450 (CYP79B2) and nitrilase (NIT) for the indole-3-acetaldoxime (IAOX) route, were identified (Figure 4A). In WP, all the metabolic genes except one TSA (Traces_5 DL_508B4718C.1, which was down-regulated in all treated samples) and YUC (Traces_5 BL_078A5 DC9C1.1) were differentially up-regulated (94%) whereas 67% of IAA metabolic genes were up-regulated in KA (Table S11). In IAA signaling pathway, majority of genes were up-regulated in all treated samples (Figure 4B). In particularly, genes encoding ARF16, which is known to regulate expression of ABI3 on ABA signaling, showed higher up-regulations in 'Woori'.  
Figure 3: Heat map analysis of DEGs from PHS and ABA treatment for gibberellic acid (GA) hormone metabolism and signaling: (**A**) hormone metabolism pathway of GAs and comparative expression of genes related to GAs hormone metabolism. All the process in blue box and red box are catalyzed by _GA20_ox and _GA30_ox, respectively; (**B**) Signaling pathway of GA and comparative expression of genes related to GA signaling. The heatmap shows an expression change compared to the controls for each cultivar, with log2 fold-change values.  
Based on our RNA-seq data, two enzymes (IPP and IPT) related to cytokinin hormone metabolism were identified (Figure 5A). One of IPTs, Traes_1 BL_5C0E7A70E.1, was upregulated in all samples while the other one, Traes_2 BS_8 FF7A4 DD7.1, was differentially up-regulated in WP and WA (Table S12). Three enzymes (HK, Type B ARR, and Type A ARR) were identified as associated protein for cytokinin signaling (Figure 5B). All the unigenes involved in the cytokinin signaling were up-regulated in all samples except one Type B ARR (Traes_4 DL_2527 CA8 BF.1) in KA (RPKM ratio = 0.887).  
Figure 4: Heat map analysis of DEGs from PHS and ABA treatment for indole-3-acetic acid (IAA) hormone metabolism and signaling: (**A**) hormone metabolism pathway of IAA and comparative expression of genes related to IAA hormone metabolism; (**B**) signaling pathway of IAA and comparative expression of genes related to IAA signaling. The heatmap shows an expression change compared to the controls for each cultivar, with log2 fold-change values.  
Figure 5: Heat map analysis of DEGs from PHS and ABA treatment for GA hormone metabolism and signaling: (**A**) hormone metabolism pathway of cytokinin and comparative expression of genes related to cytokinin hormone metabolism; (**B**) signaling pathway of cytokinin and comparative expression of genes related to cytokinin signaling. The heatmap shows an expression change compared to the controls for each cultivar, with log2 fold-change values.