Pre-Cutting Shading of Stock Plants Promotes Adventitious Rooting of Apple Dwarfing Rootstock ‘Y-1’ Softwood Cuttings

Apple is notoriously difficult to propagate by cuttings, which severely restricts the large-scale production of own-rooted dwarfing rootstocks. ‘Y-1’ is a promising apple dwarfing rootstock that has been newly bred in China, but its recalcitrant rooting limits its application as an own-rooted stock. In this study, three-year-old ‘Y-1’ stock plants were subjected to three shading rates (40%, 60% and 80%) for 7, 14 and 21 days before cutting collection, and the rooting performance, endogenous hormone and phenolic profiles, antioxidant enzyme activities, and transcriptomic responses of the shoots and cuttings were systematically investigated. Shading of stock plants significantly promoted adventitious rooting, with the combination of 60% shading for 14 days giving the highest rooting rate (39.74%), compared with 5.13% in the unshaded control at the same stage. During shading, leaf chlorophyll content increased with shading intensity and peaked at day 14; phloem indole-3-acetic acid (IAA) and gibberellin (GA3) contents remained higher than the control, whereas abscisic acid (ABA) and major phenolics (phloridzin, chlorogenic acid, quercitrin and rutin) declined. Transcriptome analysis of the phloem (full light vs. 60% shading at days 7 and 14) identified up to 10,944 differentially expressed genes (DEGs), which were significantly enriched in plant hormone signal transduction, MAPK signaling and plant–pathogen interaction pathways. Shading up-regulated auxin biosynthesis and transport genes (YUCCA6, ARG7, LAX2/LAX3, PIN2) and SAUR genes (SAUR20/50/72/78) while down-regulating auxin signaling repressors and receptors (IAA3/13/14/16/17/26/29/30, TIR1, AFB2, ARF5/6/17/19, PIN3) and the ABA-responsive factor DPBF3. During subsequent rooting, shaded cuttings exhibited four rooting phases (callus formation, root primordium induction, root emergence and elongation); higher IAA and GA3 and lower ABA and total phenols, together with earlier peaks of POD, PPO, and IAAO activities, characterized the shaded, easy-to-root cuttings. These results indicate that pre-cutting shading creates a “rooting-competent” physiological and transcriptional state in stock-plant shoots that is inherited by the cuttings, providing a practical protocol for ‘Y-1’ cutting propagation and mechanistic insight into light-mediated regulation of adventitious rooting in apple.