Leaf Color Variation in Phoebe bournei Arises from a PbUFGT9 SNP and MYB-Mediated Anthocyanin Flavonol Competition

Phoebe bournei newly emerged leaves exhibit green, yellow, or red phenotypes, whereas molecular regulatory mechanism is unknown. A total of 19,518,953 reliable single nucleotide polymorphisms (SNPs) were identified from 304 individuals from 152 half-sib families. Genome-wide association study (GWAS) revealing a key SNP in PbUFGT9 promoter was associated with color parameter a*, resulting in the alteration of the MYB-binding motif. Combined of metabolomic and transcriptomic data identified the competition between anthocyanin and flavonol biosynthesis in distinct color leaf. In red leaves, highly expressed PbMYB30 induces PbPAL1, PbCHI1, and PbUFGT9 for anthocyanin accumulation; the “G” SNP in the PbUFGT9 promoter weakens its transcriptional regulation, leading to lower anthocyanin content and green leaves. PbBBX1 and PbHY5-1 formed a transcriptional complex that synergistically activates PbMYB30. In yellow leaves, PbMYB211 regulated PbFLS, diverting flux toward flavonol biosynthesis. Notably, a* values were positively correlated with summer growth, PbUFGT9 genotype distribution was linked to the maximum temperature of the hottest month, implying red-leaf individuals have enhanced heat and drought tolerance. This multi-omics study uncovers the regulatory network of diversified leaf color, which provides theoretical and practical foundations for color and stress-tolerance improvement of P. bournei.