Comparative Transcriptome Analysis Reveals Potential Molecular Regulation of Organic Acid Metabolism During Fruit Development in Late-Maturing Hybrid Citrus Varieties

Late-maturing hybrid citrus is a significant fruit that combines the best traits of both parents and is highly prized for its unique flavor. Not only can organic acids alter the flavor of citrus pulp, but they are also essential for cellular metabolism, energy conversion, and maintaining the acidbase balance in plant tissues. Although organic acids play a key role in the quality formation of citrus fruits, there is still insufficient research on the metabolic processes of organic acids in late-maturing hybrid citrus varieties. In this study, three late-maturing citrus varieties with different acidity levels, namely ‘Huangjinjia’ (HJ), ‘Kiyomi’ (QJ), and ‘Harumi’ (CJ), were selected to systematically investigate the metabolic regulation mechanism of organic acids in late-maturing citrus through transcriptome sequencing technology, combined with physiological and biochemical analyses. This study revealed gene expression differences related to organic acid synthesis and degradation. Through gene expression profiling, several genes closely associated with organic acid metabolism were identified, and a preliminary gene network related to the regulation of organic acid metabolism was constructed. The results showed that there were significant differences in the organic acid metabolic pathways between different varieties and growth stages of the fruit. Specifically, HJ had a higher TA content than QJ and CJ, primarily due to the significantly higher citric acid and malic acid contents in HJ compared to the other two varieties. Further analysis revealed that four gene modules showed a high correlation with the levels of major organic acids in the fruits. The genes involved in these modules are closely related to organic acid synthesis, degradation, and transport. Additionally, we also identified several key genes (AS1, BZP44, COL4, TCP4, IDD10, YAB2, and GAIPB) that might be involved in the regulation of organic acid metabolism. The functions of these genes could have a significant impact on the expression levels changes of enzymes related to organic acid metabolism. This study provides a foundation for exploring the intrinsic mechanisms regulating the organic acid content in late-maturing hybrid citrus fruits and contributes to the functional research of organic acids in late-maturing hybrid citrus and the molecular design of high-quality varieties.