Elucidating nutrient composition and biosynthesis in Macadamia integrifolia through multi-omics profiling across developmental stages.

Macadamia (Macadamia integrifolia), a high-value cash crop, has garnered significant attention due to its rich nutritional profile and unique health benefits. Previous studies have primarily focused on analyzing nutritional components, without systematically elucidating the mechanisms underlying their synthesis during kernel development. To elucidate the molecular and metabolic basis of kernel quality formation, we integrated morphological, nutritional, transcriptomic, and metabolomic analyses across five developmental stages (T1-T5, 60-190 days after fruit setting). Rapid kernel expansion occurred during T1-T2, and T5 was designated as the mature stage. Compared with T1, fruit diameter and weight at T5 increased by 30% and 82%, respectively, the contents of crude fat, protein, and total amino acids increased by 10%, 30%, and 127%, respectively, whereas soluble sugar content declined by 38%. Transcription factors such as bHLH, NAC, and WRKY, together with auxin- and cytokinin-related genes, were highly expressed during T1-T2, coordinately regulating early cell expansion. Jasmonic acid accumulated markedly during both the T1-T2 period and the T5 stage, coinciding with active oil synthesis. During the T1 stage, serine and glutamate metabolism predominated, laying the foundation for protein and fatty acid biosynthesis. This metabolic program transitioned to a stress-responsive state at the T5 stage, characterized by the accumulation of proline and arginine and increased levels of ERF-family transcription factors, thereby enhancing cellular resilience to late-stage stress. Additionally, citrate and isocitrate levels peaked during oil synthesis, potentially supplying energy and acetyl-CoA for lipid biosynthesis. This study systematically elucidates the dynamic network underlying macadamia kernel development and offers actionable targets for optimizing harvest timing and breeding high-quality cultivars.