Transcriptomic and Structural Insights into Leaf Variegation Development in Ilex × ‘Solar Flare’

The mechanisms underlying leaf variegation in the ornamental <i>Ilex</i> × 'Solar Flare' remain poorly understood. To investigate this phenomenon, we conducted a comprehensive characterization of its variegated leaves. Compared to green sectors, yellow sectors exhibited severe chloroplast structural abnormalities, including swollen chloroplasts, damaged thylakoid membranes, and reduced chloroplast numbers. These yellow sectors also showed significantly lower chlorophyll and carotenoid levels, along with a depletion of key chlorophyll precursors-protoporphyrin IX (Proto IX), magnesium protoporphyrin IX (Mg-Proto IX), and protochlorophyllide (Pchlide). Photosynthetic efficiency was significantly impaired. Comparative transcriptome analysis identified 3510 differentially expressed genes (DEGs) between yellow and green sectors. Key disruptions in chlorophyll biosynthesis included upregulated <i>CHLD</i> expression and downregulated <i>CHLH</i> and <i>CHLG</i> expression, leading to impaired chlorophyll synthesis. Additionally, chlorophyll degradation was accelerated by <i>PAO</i> upregulation. Defective chloroplast development in yellow sectors was associated with the downregulation of <i>GLK1</i>, <i>GLK2</i>, and thylakoid membrane-related genes (<i>PsbC</i>, <i>PsbO</i>, <i>PsbR</i>, <i>PsaD</i>, and <i>PsaH</i>). These molecular alterations likely drive the variegated phenotype of <i>I.</i> × 'Solar Flare'. These observations advance our understanding of the genetic and physiological mechanisms regulating leaf variegation in this cultivar.