Co-Analysis of Transcriptome and Metabolome Reveals Flavonoid Biosynthesis in Macadamia Pericarp Across Developmental Stages

The pericarp of <i>Macadamia integrifolia</i> represents a promising but underexplored source of functional flavonoids. To systematically elucidate their biosynthesis and enhance the industrial potential of this by-product, we conducted integrated transcriptomic and metabolomic profiling of pericarps across five developmental stages (50, 80, 110, 140, and 170 days after flowering). Our analysis reveals, for the first time, a distinct temporal shift in both gene expression and metabolite accumulation. Early stages were characterized by high expression of PAL, <i>4CL</i>, <i>CHS</i>, and <i>FLS</i>, coupled with abundant flavonols and anthocyanins. In contrast, late stages exhibited upregulation of <i>CHI</i> and <i>F3'5'H</i>, redirecting the metabolic flux toward flavanones and isoflavones. This dynamic profile was closely associated with jasmonate and gibberellin signaling pathways and was likely regulated by key transcription factors (MYB, NAC, bHLH). These findings provide a multi-omics framework that elucidates the temporal flavonoid biosynthesis in macadamia pericarp, thereby laying the groundwork for its future industrial valorization.