
Grafting is commonly used to relieve damage caused by soil-borne diseases and to enhance the nutrient uptake in watermelon plants. Certain reports have shown the proteomic changes of plant tissues involved in grafting, while little information about the secretome after watermelon grafting is available. To gain insight into the root-secreted protein profile, root exudates of three types of seedlings (own-root watermelon (W), grafted-root watermelon (WB) and own-root bottle gourd (B)) were collected under hydroponic conditions, desalted and concentrated using Amicon ultracentrifugal filter devices, and separated by one-dimensional SDS–PAGE. Principal component analysis revealed that the protein profile was distinctly altered after grafting, and the diversity of root-secreted proteins of WB was significantly higher than that of W and B. Moreover, analysis by LC-QTOF/MS/MS revealed that some proteins associated with biotic and abiotic stress resistance appeared in response to grafting, such as disease resistance protein At4g27190, callose synthase, HVA22, and Clp protease. These results indicate that grafting can shift the root-secreted protein profile and thus could increase stress resistance. This study would help to reveal the mechanisms of disease resistance and growth promotion achieved through grafting.