## 3 Results
### DEGs Identification, GO Enrichment, and KEGG Pathway Analysis  
The number of expressed genes in the three pairs (LTL vs. LTH, STL vs. STH, FTL vs. FTH) is shown in Table S3. Fragments per kilobase of transcript per million mapped reads (FPKM) values were used to represent gene expression level, and! Fold Change! > 2 and \(p\) < 0.05 were used as thresholds for significant differentially expressed genes (DEGs) selection. The results showed that there were 539 (203 upregulated, 336 downregulated), 755 (402 upregulated, 353 downregulated), and 617 (308 upregulated, 309 downregulated) DEGs obtained in the low and high RAA content pools of the leaf, stalk and floret, respectively (Figure 1A, Table S3). The hierarchical clustering of the three plant parts of DEGsis shown in Figure 1B. Subsequently, twenty DEGs were also identified in the three plant parts simultaneously (Figure 1C, Table S4).  
To better understand the biological functions of DEGs identified between the low and high RAA content pools in three plant parts, GO enrichment analysis was used for functional classification. The result showed that DEGs classified in ontological biological processes (BPs), cellular components (CCs), and molecular functions (MFs) were obtained for the three comparison groups (Figure S3). Among the DEGs of leaf, the upregulated DEGs were mainly involved in the glucosinolate metabolic process, S-glycos metabolic process (BPs), oxidoreductase activity (MFs), and secretory vesicle (CCs) (Table S5). In the stalk, the main GO terms of upregulated DEGs were the circadian rhythm (BPs), cysteine-type endopeptidase inhibitor activity (MFs), and secretory vesicle (CCs) (Table S5). In the floret, the main GO terms of upregulated DEGs were glucosinolate metabolic process and glucosinolate biosynthetic process (BPs), sugar transmembrane transporter activity and carbohydrate transmembrane transporter activity (MFs), and the monolayer-surrounded lipid storage body (CCs) (Table S5). The above results indicated that it had homogeneity in the DEGs among different plant parts pools.  
To further investigate the potential functions of those DEGs between the low and high RAA content pools of three plant parts, KEGG pathway enrichment analyses were performed on DEGs, respectively. The top 10 enrichment pathways are visualized in Figure 2A-C. It showed that \"glucosinolate biosynthesis\" and \"biosynthesis of secondary metabolites\" were found to be significantly enriched in the three plant parts pools (Figure 2A-C); \"plant hormone signal transduction\", \"alpha-Linolenic acid metabolism\", \"linoleic acid metabolism\", and \"caffeine metabolism\" were found to be significantly enriched in leaf and stalk pools (Figure 2A,B); whereas \"2-oxocarboxylic acid metabolism\" was significantly enriched in the leaf and floret pools (Figure 2A,C). These results indicated that the different organs of  
Figure 1: Changes in DEGs expression. **(A)** Upregulation and downregulation of DEGs in LTL vs. LTH, STL vs. STH, and FTL vs. FTH. The yellow box represents upregulation, and the blue box represents downregulation. **(B)** Heatmaps of DEGs compared between different groups. **(C)** Coregulation of DEGs in all comparison groups. LTL (LTL1, LTL2, LTL3), STL (STL1, STL2, STL3) and FTL (FTL1, FTL2, FTL3) represent low RAA content pools in leaf, stalk and floret, respectively. LTH (LTH1, LTH2, LTH3), STH (STH1, STH2, STH3) and FTH (FTH1, FTH2, FTH3) represent high RAA content pools in leaf, stalk and floret, respectively.  
broccoli undertook active metabolic and genetic processes, and the enrichment analyses of the KEGG pathway provided a valuable resource for studying specific pathways and processes in broccoli.