Tangor, an important citrus type, is a hybrid of orange and mandarin and possesses their advantageous characteristics. Fruit quality is an important factor limiting the development of the citrus industry and highly depends on fruit development and ripening programs. However, fruit development and quality formation have not been completely explored in mandarin-orange hybrids. We sequenced the metabolome and transcriptome of three mandarin-orange hybrid cultivars at the early fruiting [90 days after full bloom (DAFB)], color change (180 DAFB), and ripening (270 DAFB) stages. Metabolome sequencing was performed to preliminarily identify the accumulation patterns of primary and secondary metabolites related to fruit quality and hormones regulating fruit development. Transcriptome analysis showed that many genes related to primary metabolism, secondary metabolism, cell wall metabolism, phytohormones, and transcriptional regulation were up-regulated in all three cultivars during fruit development and ripening. Additionally, multiple key genes were identified that may play a role in sucrose, citric acid and flavonoid accumulation, cell wall modification, and abscisic acid signaling, which may provide a valuable resource for future research on enhancement of fruit quality of hybrid citrus. Overall, this study provides new insights into the molecular basis of pulp growth and development regulation and fruit quality formation in mandarin-orange hybrids.

Fruit cracking affects both the yield and economic efficiency of citrus; however, the underlying mechanism remains unclear. Therefore, this study focused on resistant and susceptible cultivars to identify the mechanisms underlying fruit cracking. The results showed that in ‘Mingrijian’, pectin morphological transformation and hemicellulose and lignin degradation in the pericarp were important contributing factors. During the critical fruit-cracking period (115–150 days after flowering), the water-soluble pectin, protopectin, and lignin contents in the pericarp of ‘Daya’ presented inverse changes relative to those in ‘Mingrijian’, thus enhancing the mechanical properties and resistance of pericarp. From 115 to 150 days after flowering, the soluble sugar content in the pulp of ‘Mingrijian’ increased rapidly by 97.35%, aiding in pulp water absorption and expansion. Moreover, the soluble protein content in the pericarp of ‘Mingrijian’ exhibited a declining trend and was lower than that of ‘Daya’, thus affecting the overall metabolism. The superoxide dismutase (SOD) activity in the pericarp of ‘Mingrijian’ gradually decreased from 115 to 180 days after flowering, while the peroxidase (POD) activity remained at a low level, resulting in weaker antioxidant capacity and lower environmental resistance. This study provides valuable insights into the mechanisms of citrus fruit cracking, laying the foundation for preventive and control strategies.