Widely targeted metabolomics and physiological analyses reveal the impact of ‘Zhongmikangzhen No. 2’ rootstock on Actinidia deliciosa

• ‘Zhongmikangzhen No 2′ rootstock enhances kiwifruit fruit size. • ‘Zhongmikangzhen No 2′ improves fruit aroma through elevated levels of decanoic acid and 9-oxononanoic acid. • ‘Zhongmikangzhen No 2′ increases nutritional value by promoting α-linolenic acid accumulation. • ‘Zhongmikangzhen No 2′ raises 12-oxo-phytodienoic acid content, potentially enhancing abiotic stress resistance. Kiwifruit has extremely high nutritional value, but its rootstock strongly influences the physiology and metabolism of its scion fruit. Here, we evaluated the influence of a new kiwifruit rootstock, Actinidia valvata ′Zhongmikangzhen No. 2′, on the leaves and fruits of the scion A. deliciosa ′Zhongmi 2′. The leaf size, leaf mineral element contents, fruit size (single-fruit weight, longitudinal diameter and transverse diameter), and fruit quality traits (soluble sugar content, vitamin C content, total acidity and dry matter content) of ′Zhongmi 2′ grafted on ′Zhongmikangzhen No. 2′ (zk) and A. deliciosa seedling (zp) rootstock were measured at five fruit developmental stages (30, 60, 90, 120, and 150 days after flowering (DAF)). The zk fruits were significantly larger than those of zp and their leaves were also longer. The leaf length and width of the zk fruits was significantly greater than those of the zp fruits. The leaf contents of Cu, P and Mo significantly differed at 60, 120 and 120 DAF, respectively. The fruits of the two stock–scion combinations may presented different flavors. UPLC–MS/MS analysis of the fruit metabolome revealed 1697 differentially expressed metabolites. These metabolites, which were divided into multiple categories through KEGG analysis, indicated significant differences in fruit quality and resistance. Decanoic acid (decreased in zk-hard) and 9-oxononanoic acid (increased in zk-hard) may collectively affect fruit aroma. Moreover, α-linolenic acid and 12-oxo-phytodienoic acid (a precursor of jasmonic acid), both of which increase in zk-hard, contribute to increased nutritional value and are involved in the abiotic stress response, respectively. This study revealed the effects of different rootstock–scion combinations on fruit quality traits and leaf mineral elements and provides a basis for studying the mechanisms of rootstock–scion interactions.