Integrated Transcriptomic and Metabolomic Analysis Reveals Key Genes in Fatty Acid and Flavonoid Biosynthesis in Macadamia Nut (Macadamia integrifolia)

bHLH transcription factors are central to plant development and to the metabolism of fatty acids and flavonoids. Through the transcriptomic, metabolomic, and phytohormone/elemental profiling of two macadamia varieties with divergent fatty acid content, ‘Guire No. 1’ (GR1) and ‘A4’, we identified 142 MibHLH transcription factors, classified into 21 subfamilies, of which 14 show collinearity with Arabidopsis AtbHLH members. MibHLH46 was markedly differentially expressed, and its expression strongly correlated with that of fatty acid biosynthesis genes. Promoter analysis further revealed abundant MYC and G-box elements in fatty acid and flavonoid biosynthetic genes. Comparative metabolomics showed that ‘GR1’ accumulates higher levels of several mineral elements (Fe, Ca, Mg) and abscisic acid (ABA) than ‘A4’. These transcriptomic trends were confirmed by qRT-PCR, which validated the up-regulation of genes related to fatty acid oxidation, α-linolenic acid metabolism, and the flavonoid pathway in ‘GR1’. We propose that MibHLH46, as a candidate regulator, contributes to kernel fatty acid and flavonoid metabolism by transcriptionally regulating key biosynthetic genes, providing a basis for identifying regulatory genes in macadamia lipid metabolism.