Characterization of Goji Quality at Different Harvest Stages in Qaidam Basin Based on Transcriptome and Widely Targeted Metabolome

Goji, a renowned traditional Chinese medicine and food source, is characterized by a long fruiting period. This study was conducted to investigate the variations in nutritional quality of goji berries across different harvest stages by utilizing widely targeted metabolome and transcriptome. The results showed that goji berries of the first harvest stage had advantages in terms of size and metabolic levels, and there was little difference in sugars and organic acids levels. Within significantly enriched phenylpropanoid and flavonoid pathways, chlorogenic acid, and its positional isomers (neochlorogenic acid and cryptochlorogenic acid) increased significantly along with P‐coumaroyl quinic acid as the harvest stages progressed, while the other bioactive DEMs including scopoletin, scopolin, naringenin, and pruning exhibited a decreasing trend. The key DEGs encoding PAL, HCT, 4CL, C4H, TOGT1, and C12RT1 were suggested to regulate the variations of these DEMs. Furthermore, six oxidative metabolites enriched in alpha‐linolenic acid and linoleic acid metabolism pathways all peaked at the second harvest stage. Climate or plant weakening is suggested as potential factors influencing the metabolic and transcriptomic changes in goji berries. This study provides a fresh perspective on understanding the accumulation of metabolites and their molecular mechanisms in goji at different harvest stages in the Qaidam Basin and can be used to guide goji production and processing.