## 5 Conclusions
Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification of differential accumulated metabolites (DAMs) in LML vs. LMH (A), SML vs. SMH (B), and FML vs. FMH (C) pools. The \(X\)-axis is the number of annotated genes to different categories of KEGG. The \(Y\)-axis represents different categories of KEGG. Blue column, Metabolism systems; Brown column, Environmental information processing. LML, SML and FML represent low RAA content pools in leaf, stalk and floret, respectively. LMH, SMH and FMH represent high RAA content pools in leaf, stalk and floret, respectively. Figure S8. KEGG pathway of DAMs in LML vs. LMH (A), SML vs. SMH (B), and FML vs. FMH (C) pools. The \(X\)-axis is the rich factor; the \(Y\)-axis represents the name of the pathway. The bubble size represents the number of DAMs involved. The bubble color indicates the enrichment degree of pathway and the size represents the number of DAMs enrichment in the pathway. LML, SML and FML represent low RAA content pools in leaf, stalk and floret, respectively. LMH, SMH and FMH represent high RAA content pools in leaf, stalk and floret, respectively. Figure S9. Correlation analysis between transcriptome and metabolome in LML vs. LMH and SML vs. SMH. The nine-quadrant diagram shows the correlation of genes and compounds between LML and LMH (A), SML and SMH (B). KEGG enrichment analysis of DEGs (red column) and DAMs (blue column) enriched in the same pathway in LML vs. LMH (C), SML vs. SMH (D). LML and SML represent low RAA content pools in leaf and stalk, respectively. LMH and SMH represent high RAA content pools in leaf and stalk, respectively. Table S1. Types and contents of glucosinolates in the two parental lines. Table S2. Sequencing, assembly statistics and comparative efficiency statistics for the 3 pairs transcriptomes of leaf, stalk and floret, respectively. Table S3. Summary of the DEGs and DAMs among 3 library pairs. Table S4. Twenty co-regulated DEGs statistics. Table S5. The top ten GO pathways of DEGs enrichment degree. Table S6. Differentially expressed genes related to glucosinolates synthesis process between low and high pools. Table S7. Primer sequences used in qRT-PCR analysis. Table S8. Categories of the metabolites identified in leaf, stalk and floret of F2 plants, respectively. Table S9. Co-regulated differential metabolites in leaf, stalk and floret. Table S10. DEGs related to plant hormone signal transduction between high and low RAA content. Table S11. DAMs related to flavonoids between high and low RAA content. Table S12. DEGs related to flavonoid biosynthesis between high and low RAA content. References [50; 51; 52] are listed in Table S11. Conceptualization, X.T. and H.H. ; methodology, X.T. and X.Y. ; software, X.T. and B.C. ; validation, X.T. and H.H. ; formal analysis, X.T. and L.H. ; investigation, X.T. ; resources, X.T. and Y.D. ; data curation, X.T. and Y.W. ; writing--original draft preparation, X.T. ; writing--review and editing, H.H. and G.L. ; visualization, X.T. and Y.W. ; supervision, H.H. ; project administration, X.T. and G.L. ; funding acquisition, X.T., H.H., Y.D. and G.L. All authors have read and agreed to the published version of the manuscript. This research was supported by the Innovation and Capacity Building Project of Beijing Academy of Agriculture and Forestry Sciences (KJCX20200213, KJCX20220419), the National Key Research and Development Program of China (2022 YFF1003000), and Beijing Postdoctoral Research Foundation (130220061). Not applicable. Data Availability Statement: The datasets presented in this study can be found in the Genome Sequence Archive in BIG Data Center ([[https://bigd.big.ac.cn/](https://bigd.big.ac.cn/)]([https://bigd.big.ac.cn/](https://bigd.big.ac.cn/)), accessed on 25 November 2022), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under the accession number: CRA00927. The authors declare no conflict of interest.