Abstract
Anthocyanins are plant pigments that contribute to fruit coloration and nutritional quality, yet the coordinated regulation of their accumulation in both peel and flesh remains elusive. Here, we present a haplotype-resolved genome of Malus cv. 'Royalty', a model cultivar with consistently red peel and flesh. A zinc-finger transcription factor, MdZAT5, was identified as a candidate regulator of anthocyanin biosynthesis, with two copies located on chromosomes 3 and 11 in each haplotype, as revealed by a well-assembled genome and transcriptomic profiling. Promoter and expression analyzes indicated that MdZAT5-3G acts downstream of light and MeJA signalling pathways. Transgenic analysis showed that MdZAT5-3G significantly promotes anthocyanin accumulation and upregulates anthocyanin biosynthesis genes such as MdCHS, MdCHI, and MdF3H, whereas its knockdown leads to reduced pigmentation. In contrast, MdZAT5-11G lacks regulatory function in both peel and flesh. Downstream binding assays confirmed that MdZAT5-3G directly binds to the promoters of anthocyanin biosynthetic genes, and biochemical assays revealed that its interaction with MdHY5 enhances promoter binding and transcriptional activation.