Root elongation is a key adaptive trait that enables plants to respond to soil conditions and is jointly regulated by auxin signaling and very long-chain fatty acids (VLCFAs). However, the molecular mechanism underlying this pathway remains unclear in apple. In this study, we elucidate the roles and regulatory relationship between auxin and VLCFA biosynthesis in apple. VLCFA accumulation increases auxin levels in roots, reduces the expression of IAA-related genes, and promotes root morphogenesis. This interaction refines the conventional view of auxin as the sole regulator of root development and reveals a synergistic auxin–VLCFA regulatory network that integrates hormonal signaling with metabolic control.

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