Genome Assembly Revealed MdZAT5 Coordinates Anthocyanin Biosynthesis in Apple Fruit Peel and Flesh by Interacting With MdHY5

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.