Comparative proteomic analyses provide novel insights into the effects of grafting wound and hetero-grafting per se on bottle gourd

• Effects of wound and grafting per se were readily distinguishable at proteome level.
• Effects of grafting per se were different between graft union and upper vicinity.
• Hydrogen peroxide might play an important signaling role in hetero-grafting systems.

Grafting is a technology widely used in agriculture and biological research. During a hetero-grafting process, cutting wound and hetero-grafting per se are the two main stimuli invoking cellular and whole-plant responses. Despite the importance of dissecting the individual effects of the two in adequately interpreting experimental data, no currently published data are dedicated to comparing the effects of hetero-grafting per se and grafting wound. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) technique-based proteomic analyses were conducted between various scion-rootstock combinations of bottle gourd. Our results demonstrated that effects of grafting wound and hetero-grafting per se were readily distinguishable at the proteome level. Grafting wound affected the proteomes differentially at the graft union and its upper vicinity. Its effects were also likely related to the stress resistance level of each genotype. The effects of hetero-grafting per se on proteome were markedly different between graft union and the upper vicinity. This study provides an explicit evidence for the effectiveness of the commonly used methods of eliminating the effects of grafting wound in a hetero-grafting system by setting up a homo-grafted control. The role of hydrogen peroxide as a signal molecule in hetero-grafting systems is suggested.