Drought stress is one of the main abiotic stresses that limit plant growth and affect fruit quality and yield. Plants primarily lose water through leaf transpiration, and wax effectively reduces the rate of water loss from the leaves. However, the relationship between water loss and the wax formation mechanism in goji (Lycium barbarum) leaves remains unclear. ‘Ningqi I’ goji and ‘Huangguo’ goji are two common varieties. In this study, ‘Ningqi I’ goji and ‘Huangguo’ goji were used as samples of leaf material to detect the differences in the water loss rate, chlorophyll leaching rate, wax phenotype, wax content, and components of the two materials. The differences in wax-synthesis-related pathways were analyzed using the transcriptome and metabolome methods, and the correlation among the wax components, wax synthesis genes, and transcription factors was analyzed. The results show that the leaf permeability of ‘Ningqi I’ goji was significantly lower than that of ‘Huangguo’ goji. The total wax content of the ‘Ningqi I’ goji leaves was 2.32 times that of the ‘Huangguo’ goji leaves, and the epidermal wax membrane was dense. The main components of the wax of ‘Ningqi I’ goji were alkanes, alcohols, esters, and fatty acids, the amounts of which were 191.65%, 153.01%, 6.09%, and 9.56% higher than those of ‘Huangguo’ goji, respectively. In the transcriptome analysis, twenty-two differentially expressed genes (DEGs) and six transcription factors (TFs) were screened for wax synthesis; during the metabolomics analysis, 11 differential metabolites were screened, which were dominated by lipids, some of which, like D-Glucaro-1, 4-Lactone, phosphatidic acid (PA), and phosphatidylcholine (PE), serve as prerequisites for wax synthesis, and were significantly positively correlated with wax components such as alkanes by the correlation analysis. A combined omics analysis showed that DEGs such as LbaWSD1, LbaKCS1, and LbaFAR2, and transcription factors such as LbaMYB306, LbaMYB60, and LbaMYBS3 were strongly correlated with wax components such as alkanes and alcohols. The high expression of DEGs and transcription factors is an important reason for the high wax content in the leaf epidermis of ‘Ningqi I’ goji plants. Therefore, by regulating the expression of wax-synthesis-related genes, the accumulation of leaf epidermal wax can be promoted, and the epidermal permeability of goji leaves can be weakened, thereby reducing the water loss rate of goji leaves. The research results can lay a foundation for cultivating drought-tolerant goji varieties.
