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Climate changes especially chilling stress affects cucurbit crops during winter seasonal production. Grafting to pumpkin rootstocks is widely used to improve the vigor of cucurbits, especially cucumber (Cucumis sativus L.) plants, in the face of chilling stress. In our study, multi-disciplinary aspect approaches were used to investigate growth changes of pumpkin under chilling stress. Firstly, the morphological and physiological characteristics of 14 pumpkin (Cucurbita moschata) varieties following different periods of chilling stress was analyzed by using physiological means. Mathematical results of principal component analysis (PCA) with chlorophyll-a, chlorophyll-b, carotenoid contents, chilling injury index and relative electrolyte permeability indicated that relative electrolyte permeability as the primary judgment index was best associated with the comparison of chilling tolerance in pumpkin rootstock varieties. Then, transcriptomic and DCMU (Diuron) application and chlorophyll fluorescence examination analysis of pumpkin leaves revealed that 390 Cucurbita moschata differentially expressed genes (CmoDEGs) that affect photosynthesis were upregulated in leaves. 127 CmoDEGs both in leaves and roots were enriched for genes involved in unsaturated fatty acid metabolism, suggesting that plasma membrane lipids are involved in chilling perception. The results of increased composition of unsaturated fatty acid in leaves and qRT-PCR analysis of relative mRNA abundance confirmed that α-linolenic acid biosynthesis was responding to pumpkin chilling tolerance. The integration of physiological, mathematical bioinformatical and biological analysis results contributes to our understanding of the molecular mechanisms underlying chilling tolerance and its improvement in cucumber grafted on pumpkin rootstocks. It provided an important theoretical basis and reference for further understanding on the impact of climate change on plant physiological changes.

Grafting is widely used in fruit, vegetable, and flower propagation to improve biotic and abiotic stress resistance, yield, and quality. At present, the systemic changes caused by grafting, as well as the mechanisms and effects of long-distance signal transport between rootstock and scion have mainly been investigated in model plants (Arabidopsis thaliana and Nicotiana benthamiana). However, these aspects of grafting vary when different plant materials are grafted, so the study of model plants provides only a theoretical basis and reference for the related research of grafted vegetables. The dearth of knowledge about the transport of signaling molecules in grafted vegetables is inconsistent with the rapid development of large-scale vegetable production, highlighting the need to study the mechanisms regulating the rootstock-scion interaction and long-distance transport. The rapid development of molecular biotechnology and “omics” approaches will allow researchers to unravel the physiological and molecular mechanisms involved in the rootstock–scion interaction in vegetables. We summarize recent progress in the study of the physiological aspects (e.g., hormones and nutrients) of the response in grafted vegetables and focus in particular on long-distance molecular signaling (e.g., RNA and proteins). This review provides a theoretical basis for studies of the rootstock–scion interaction in grafted vegetables, as well as provide guidance for rootstock breeding and selection to meet specific demands for efficient vegetable production.