The apple anthocyanin content is an important trait in apple breeding. Auxin, as an important plant hormone, plays significant roles in regulating the biosynthesis of anthocyanins. However, the molecular mechanism of how plants regulate auxin content and activity to affect anthocyanin accumulation remains unclear. In this study, through fruit anthocyanin content analysis and transcriptome sequencing of the hybrids derived from ‘Golden Delicious’ and ‘Fuji Nagafu No. 2’ crosses, a key gene for regulating apple anthocyanin accumulation, indole-3-acetic acid (IAA) methyltransferase (MdIAMT), was identified. Functional analyses showed that the apple calli and peel overexpressing MdIAMT accumulated more anthocyanin than that in Vec by regulating IAA homeostasis. Yeast two-hybrid assays, luciferase complementation imaging assays and co-immunoprecipitation assays revealed that MdCSN5, an important protein in light signal transduction, interacts with MdIAMT. More importantly, further research showed that the MdCSN5-MdIAMT module affected auxin signal transduction pathway by regulating IAA homeostasis, thus promoting anthocyanin accumulation. In summary, our findings elucidate a novel mechanism by which auxin-regulated anthocyanin accumulation via MdCSN5-MdIAMT module, deepening our knowledge of plant hormone signaling in anthocyanin biosynthesis.

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