The present study aimed to evaluate the quality of Cynomorium songaricum Rupr. from different producing areas, which is an edible, holoparasitic, and desert plant that has been used in traditional medicine for improving immunity and kidney function and treating constipation. We optimized the extract conditions by response surface methodology (RSM) and determined the content of gallic acid, protocatechuic acid, and catechin of C. songaricum simultaneously from different producing areas by high-performance liquid chromatography (HPLC). It is the first study in which the RSM was used to optimize the extract condition of C. songaricum with multiple evaluation factors, ensuring the efficiency and accuracy of the study. The results were analyzed by principal component analysis, and they showed that the quality of C. songaricum from Qinghai Province was the best, while the quality of C. songaricum from Gansu Province was the worst. For the first time, the two ecotypes of C. songaricum, including Outside Great Wall type and Inside Great Wall type, were discovered and identified by the chemical marker protocatechuic acid. This study is the scientific basis for quality evaluation, especially for food safety.
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