Hawk tea ( var. ), derived from the tender shoots or leaves, rich in flavonoids can promote healthcare for humans. The primary flavonoid are kaempferol-3-O--D-glucoside, kaempferol-3-O--D-galactoside, quercetin-3-O--D-glucoside, and quercetin-3-O--D-galactoside. The existence of an association between leaf phenotype and flavonoid content, along with the underlying mechanisms of flavonoid biosynthesis, remains incompletely understood. In this study, 109 samples were analyzed to determine the correlation and genetic variability in leaf phenotype and flavonoid content. Furthermore, a transcriptome-wide association study identified candidate loci implicated in the biosynthesis of four key flavonoids. The study revealed that genetic variability in leaf traits and flavonoid concentrations is predominantly attributed to interpopulation differences. Flavonoid accumulation was significantly correlated with tree DBH, indicative of age-related traits. Transcriptome-wide association analysis identified 84 significant SNPs associated with flavonoid content, with only 13 located within gene regions. The majority of these genes are implicated in metabolic processes and secondary metabolite biosynthesis. Notably, structural genes within these regions are directly involved in pathways known to regulate flavonoid metabolism, exerting a pivotal influence on flavonoid biosynthesis. These results revealed the physiological basis for the regulation of flavonoid content, as well as the molecular mechanisms for the biosynthesis of flavonoids in hawk tea. It also lays theoretical groundwork for subsequent explorations into the genetic determinants influencing flavonoid accumulation of hawk tea.
