Integrated Transcriptomic and Metabolomic Analysis of Color Changes in Maize Root Systems Treated with Methyl Jasmonate

(1) Background: As a high-biomass cereal crop, maize provides substantial raw materials for food, animal feed, and processing industries. Plant root systems, vital for nutritional support, are directly vulnerable to diverse stressors that result in developmental abnormalities. Anthocyanins function as essential antioxidants, serving not only as natural pigments, but also playing crucial roles in plant stress resistance. As an essential plant hormone, jasmonic acid (JA) mediates plant stress adaptation and developmental processes, and is frequently employed to stimulate anthocyanin production. (2) Methods: Due to scarce reports on JA functions in maize, we specifically examined JA-triggered developmental regulation and anthocyanin biosynthesis using transcriptomic and metabolomic analysis. (3) Results: Phenotypic analyses revealed that exogenous JA application promoted culm development and intensified pigmentation, while enlarging the areas of stems and primary roots. Combined with phenotypic variations, our integrated transcriptomic and metabolomic analyses of root tissues also indicated that significantly altered metabolites specifically clustered within the flavonoid biosynthesis pathway. Moreover, GO and KEGG enrichment analyses of the associated differentially expressed genes confirmed their participation in this synthetic pathway with high confidence. These findings strongly suggest that methyl jasmonate (MeJA) exposure primarily modulates flavonoid biosynthesis, particularly through regulation of <i>F3H</i> and <i>DFR</i> gene expression, thereby enhancing flavonoid/anthocyanin accumulation in roots. Additionally, our correlation analysis of transcription factors revealed that <i>Zm00001d018097 (MYB)</i>, <i>Zm00001d029963 (MYB)</i>, and <i>Zm00001d000236 (bHLH)</i> likely participate in regulating the expression of structural genes, thereby promoting the upregulation of functional gene expression. (4) Conclusions: These results provide a robust framework for deciphering the MeJA-mediated regulation of anthocyanin biosynthesis in maize radicles, specifically demonstrating that <i>Zm00001d018097 (MYB)</i>, <i>Zm00001d029963 (MYB)</i>, and <i>Zm00001d000236 (bHLH)</i> coordinately enhance the expression of <i>F3H</i> and <i>DFR</i>.