Identification and quality evaluation of Citrus reticulata cv. Chachiensis varieties based on SNP markers

The desiccative and mature pericarp of Citrus reticulata cv. Chachiensis (PCRC) contenting rich flavonoids and volatile oil is used as traditional Chinese medicine. However, the biological and mechanical mixing of germplasm seriously affects the quality and clinic efficacy of PCRC. In this study, an identification system based on SNP markers was established which is capable of effectively distinguishing between two main C. reticulata cv. Chachiensis (CRC) varieties of DaZhongyoushen (DZ) and XiZhongyoushen (XZ). Moreover, mechanical mixing was confirmed to exist in another major cultivar DaDong5 (DD). Although the morphological characteristics of DZ and XZ fruits were similar, differences were observed in the contents and compositions of bioactive metabolites between the pericarps of these two CRC varieties. The content of flavonoids, especially hesperidin, in the DZ pericarp was significantly higher than that in the XZ pericarp (P < 0.01). The XZ pericarp contained many specific volatile compounds, and its volatile oil content was slightly higher than that of the DZ pericarp. In conclusion, DZ is more suitable as raw material for producing medicinal PCRC, while XZ is more promising for the development of fragranced products such as Ganpu tea. This study provides the theoretical basis and technical support for the identification and evaluation of CRC germplasm resources, which is instrumental for CRC germplasm resource innovation, further promoting the production of high-quality PCRC.