Integrating Physiology, Cytology, and Transcriptome to Reveal the Leaf Variegation Mechanism in Chia E Yenlin Variegata Leaves.

orchids, with their unique appearance and extended flowering period, are among the most commercially valuable Orchidaceae worldwide. Particularly, the variegation in leaf color of significantly enhances the ornamental and economic value and knowledge of the molecular mechanism of leaf-color variegation in is lacking. In this study, an integrative analysis of the physiology, cytology, and transcriptome profiles was performed on Chia E Yenlin Variegata leaves between the green region (GR) and yellow region (YR) within the same leaf. The total chlorophyll and carotenoid contents in the YR exhibited a marked decrease of 72.18% and 90.21%, respectively, relative to the GR. Examination of the ultrastructure showed that the chloroplasts of the YR were fewer and smaller and exhibited indistinct stromal lamellae, ruptured thylakoids, and irregularly arranged plastoglobuli. The transcriptome sequencing between the GR and YR led to a total of 3793 differentially expressed genes, consisting of 1769 upregulated genes and 2024 downregulated genes. Among these, the chlorophyll-biosynthesis-related genes , , , and showed downregulation, while the chlorophyll-degradation-related gene had an upregulated expression in the YR. Plant-hormone-related genes and transcription factors MYBs (37), NACs (21), ERFs (20), bHLH (13), and GLK (2), with a significant difference, were also analyzed. Furthermore, qRT-PCR experiments validated the above results. The present work establishes a genetic foundation for future studies of leaf-pigment mutations and may help to improve the economic and breeding values of .