Integrated transcriptomic and metabolomic profiles analysis reveals a potential gene-metabolite network associated...

Anthocyanins are important flavonoid pigments responsible for coloration in maize kernels and are associated with nutritional and health-promoting properties. This study integrated metabolomic and transcriptomic analyses to investigate the biochemical and genetic basis of kernel pigmentation in three maize inbred lines with distinct kernel colors: yellow (Yellow-K), red (Red-K), and purple (Purple-K). Phenotypic and biochemical analyses revealed that anthocyanins accumulated exclusively in the pericarp of Red-K and in both pericarp and aleurone layers of Purple-K, with total anthocyanin content highest in Purple-K. Metabolomic profiling identified 1,845 differentially accumulated metabolites (DAMs) common across all comparisons, with flavonoids and anthocyanins significantly more abundant in colored kernels. Genotype-specific divergence in anthocyanin biosynthetic flux and decorative modifications showed that Purple-K specialized in malonylation and sambubiosylation, with massive accumulation of Pg3DiMalG; Red-K specialized in rutinosylation and 5-O-glycosylation. Transcriptome analysis identified differentially expressed genes (DEGs), of which 22 structural genes, including PALs, FHT1, PR1, A1, A2, BZ1, BZ2, were coordinately upregulated in Purple-K and Red-K, showing expression patterns highly correlated with metabolite levels. Integrated omics analysis further identified 101 transcriptional regulators, including 4 MYB and 10 bHLH transcription factors (e.g., R1, PL1) with expression correlated with anthocyanin accumulation. Downregulation of JAZ repressors in pigmented kernels, along with upregulation of R1 and other bHLH factors, were observed. Together, these findings suggest that the differential accumulation of specific anthocyanin metabolites, coordinated upregulation of structural genes, and involvement of key transcription factors collectively associated with kernel color variation. This study provides insights into the potential molecular mechanisms underlying anthocyanin-based pigmentation in maize and provides a useful resource for breeding programs aiming to improve nutritional quality and visual traits in maize germplasm.