Allelic variation in LcARF10 toggles an auxin-responsive MYB70–ARF10 repressor switch governing litchi fruit acidity

Fruit acidity, a key quality trait, is primarily determined by malic acid in many fruit crops. However, the molecular machinery governing its accumulation, particularly in response to hormonal cues like auxin, remains a "black box." Here, we systematically deconstruct the regulatory pathway controlling malic acid in litchi (Litchi chinensis). We first identify the tonoplast-localized transporter LcALMT1 as the principal channel for malate sequestration into the vacuole. We then uncover its upstream regulatory module, revealing that the R2R3-MYB transcription factor LcMYB70 directly binds the LcALMT1 promoter but lacks intrinsic transcriptional activity. Instead, LcMYB70 functions as a molecular scaffold to recruit the Auxin Response Factor LcARF10, which confers transcriptional repression upon the complex. This LcMYB70-LcARF10 repressor module is negatively regulated by auxin signaling, providing a direct molecular link between the decline in endogenous auxin during fruit maturation and the attenuation of malate accumulation. Critically, we identified a single-nucleotide polymorphism in the LcARF10 gene that governs the divergence between high- and low-acid cultivars. The functional C allele in low-acid cultivars enables the formation of the repressor complex. In contrast, the T allele in high-acid cultivars contains a premature stop codon that results in a non-functional, truncated protein, preventing complex assembly and causing the high-acid phenotype. Our study defines a complete pathway from hormone to trait and its genetic basis, revealing a novel MYB-ARF scaffold module; a definitive molecular link between auxin withdrawal and metabolic reprogramming; and the functional integrity of a corepressor as a new paradigm for trait diversification.