Physiological, transcriptomic, and genetic variation analyses reveal the mechanisms underlying the yellow leaf phenotype of Kolkwitzia amabilis ‘Dream Catcher’

Leaf color mutants hold significant values in scientific research and landscape ornamentation. The underlying mechanisms are complex, and the molecular basis and physiological effects remain largely unclear. In this study, we integrated physiological traits analysis, anatomical observation, comparative transcriptomics, and sequence variation screening to elucidate the molecular and physiological differences between the normal type and the yellow-leaves mutant (‘Dream Catcher’, DC) of Kolkwitzia amabilis . Compared with the wild type, DC exhibited a significant reduction in chlorophyll content and net photosynthetic rate, thinner palisade tissue and main veins, along with disorganized mesophyll cell arrangement. Transcriptomic analysis revealed that differentially expressed genes (DEGs) were primarily enriched in pathways related to photosynthesis, ribosome biogenesis, and amino acid metabolism. Sequence variations in DC were mainly located in intergenic regions, as well as the upstream/downstream regulatory regions of genes involved in stress adaptation and secondary metabolite synthesis. Notably, mutations were identified in key chlorophyll synthesis genes, including CAO, PPOX and ChlH . Our findings suggest that the yellow-leaf phenotype of DC results from multiple factors, encompassing sequence variations and regulatory network alterations in pigment synthesis, photosynthesis system, and chloroplast development. • Wild-type and yellow mutant exhibited distinct physiological traits. • DEGs related to photosynthesis and ribosome biogenesis were significantly enriched. • Genetic variant differences are observed between wild-type and yellow-leaved plants.