Integrated metabolomic and transcriptomic analysis of the mechanism underlying pericarp variegation in Citrus reticulata ‘Gonggan’

Introduction Understanding the molecular mechanisms underlying fruit color variation is crucial for citrus breeding. The variegated ‘Gonggan’ mandarin ( Citrus reticulata Blanco) exhibits distinct phenotypic differences compared to the normal cultivar. However, the physiological and genetic basis for this variation remains unclear. Methods In this study, we integrated physiological measurements, liquid chromatography-mass spectrometry (LC-MS), and transcriptome sequencing to characterize the pericarp of the variegated ‘Gonggan’ mandarin during early fruit development stage. Results Compared with the normal ‘Gonggan’ mandarin, lightness and chromaticity values of the pericarp color exhibited significantly elevated in the variegated ‘Gonggan’ mandarin. Physiological assays revealed a drastic reduction in chlorophyll a and b contents (by 75.76% and 58.33%, respectively) and a moderate increase in total carotenoids (28.61%) in the variegated ‘Gonggan’ mandarin. Notably, phytoene accumulation in the pericarp of the variegated ‘Gonggan’ mandarin was 44.35-fold higher than that in the normal fruit, while metabolites in the middle and downstream pathway of carotenoid biosynthesis such as β-carotene and lutein were significantly reduced. Transcriptome analysis identified 1,438 differentially expressed genes (DEGs), which were predominantly enriched in metabolic pathways, secondary metabolite biosynthesis and photosynthesis. Specifically, 3 chlorophyll degradation genes encoding chlorophyll b reductase gene, chlorophyllase and SGR protein, 23 photosynthesis genes ( PsaD , PsaE , PsbO , etc .), and 6 photosynthesis-antenna proteins ( Lhca1 , Lhca2 , Lhcb1 , etc .) were significantly upregulated. Furthermore, 13 DEGs associated with plant hormone signal transduction exhibited differential expression patterns. Discussion Our findings demonstrate that the disruption of the chlorophyll degradation pathway and carotenoid biosynthesis pathway are the primary causes of the pericarp color variation in the variegated ‘Gonggan’ mandarin. This study provides novel insights into the regulatory network governing pericarp coloration and establishes a foundation for future molecular breeding strategies targeting citrus appearance quality.