MdARF16/17 link auxin signaling to Ma1-independent control of vacuolar malate transport in apple

Auxin is a central plant hormone, and organic acids are key determinants of fruit acidity and flavor; however, the molecular mechanism connecting auxin signaling to organic acids remains elusive. Here, we report a negative correlation between auxin levels and malate, the predominant organic acid in apple (Malus domestica), in progenies of "Gala" × "Mato 1" and across fruit developmental stages. This suggests that auxin reduces malate levels independently of Ma1, an aluminum-activated malate transporter (ALMT) gene that is the causal gene for the major quantitative trait locus (QTL) determining fruit acidity in apple. Integrated bulked segregant analysis and RNA-seq identified MdARF16 and MdARF17 as auxin-responsive transcription factors that repress malate accumulation. Auxin represses 2 tonoplast-localized malate transporter genes, the ALMT gene MdALMT9L and the gene MdMATEL2, which encodes a functionally distinct multidrug and toxic compound extrusion protein. However, auxin does not repress Ma1. This repression requires the cooperative action of MdARF16 and MdARF17, which directly bind the promoters of the malate transporter genes to inhibit transcription. Decreased malate transporter levels then restrict cytosolic-to-vacuolar malate transport. These findings reveal a Ma1-independent auxin-MdARF16/17 pathway controlling vacuolar malate transport in apple, offering a molecular framework for the auxin-responsive improvement of organic acid traits.