Integrated genomic and transcriptomic analysis reveals the mechanisms underlying leaf variegation in ‘Gonggan’ mandarin

Abstract

Background: The ‘Gonggan’ mandarin, an elite local cultivar from Zhaoqing City, Guangdong Province, combines the qualities of mandarin and sweet orange. A leaf-variegated mutant enhances its ornamental and economic value, providing an excellent model for studying chloroplast development and photosynthetic pigment metabolism in citrus. Results: We found that, in this variegated mutant, chloroplasts are severely deficient or absent in mesophyll cells. Physiological assessments revealed lower levels of chlorophyll, carotenoids, net photosynthetic rate (Pn), and stomatal conductance (Gs), alongside significantly higher non-photochemical quenching (NPQ) and the non-photochemical quenching coefficient (qN), reflecting increased photoprotective energy dissipation. To uncover the molecular basis of leaf variegation, high-quality genome assemblies and transcriptomes were generated for both the normal and variegated ‘Gonggan’ mandarin, enabling comparative multi-omics analysis. Key genes involved in chloroplast development, such as TOC159, PDV2, THA8, and SIG5, were downregulated in the variegated leaves. Similarly, structural genes linked to chlorophyll degradation, including CLH2, SGR, NOL, and NYC1, exhibited altered expression. Downregulation of transcription factors GLK, GNC, and GNC-LIKE (GNL), known regulators of chloroplast development and chlorophyll biosynthesis, was also observed. Conclusions: These findings suggest that disrupted expression of critical genes impacts chloroplast development and pigment metabolism, causing the leaf variegation phenotype. Overall, this study lays a foundation for functional genomics research and potential germplasm improvement of ‘Gonggan’ mandarin, and provides new insights into the mechanisms driving color variation in citrus.