Unraveling genotype-dependent metabolic and transcriptional differences between yellow and orange senescent leaves of Pistacia chinensis via multi-omics analysis

Leaf color differentiation during plant senescence is a phenotypic hallmark of metabolic reprogramming and adaptive strategy integration. However, the metabolic and transcriptomic changes in senescent leaves of different colors have not been systematically elucidated. This study investigated yellow and orange senescent leaves of Pistacia chinensis using integrated transcriptomics, targeted metabolomics, and bioinformatics analyses to reveal the core mechanisms underlying phenotypic divergence. Leaves from yellow-senescing trees are characterized by the activation of WRKY and NAC transcription factor. In contrast, leaves from orange-senescing trees relied on R2R3-MYB-regulated flavonoid biosynthesis. The genes involved in the biosynthesis and degradation of carotenoid precursors were upregulated, suggesting that the balance of these processes was maintained through a potential feedback regulatory mechanism. Metabolomic profiling indicated significantly higher levels of flavonoids in orange leaves compared to their yellow counterparts, while yellow leaves exhibited lutein-dominated metabolic patterns. These findings offer data-supported insights into the adaptive evolution theory concerning leaf color diversity during plant senescence.