Interannual Variation of Stomatal Traits Impacts the Environmental Responses of Apple Trees

Stomata are fundamental to plant-water relations and represent promising targets to enhance crop water-use efficiency and climate resilience. Here, we investigated stomatal density (SD) variation in 269 apple accessions across 3 years (2019–2021), which demonstrated significant differences between accessions but consistency over time. We selected 2 subsets of 20 accessions, each with contrasting SD: high stomatal density (HSD; 370–500 mm⁻²) and low stomatal density (LSD; 192–316 mm⁻²). SD groups were compared in stomatal function, leaf physiology and crop productivity across two seasons (2021–2022). LSD had lower stomatal conductance (g_s) and higher intrinsic water-use efficiency in both years (p < 0.05). Hotter and drier conditions in 2022 reduced g_s similarly in both groups (−22% HSD, −21% LSD), but also created a difference in net carbon assimilation (A_net) that was not present in 2021 (HSD + 1.7 μmol CO₂ m⁻² s⁻¹, p < 0.05). LSD constraints on A_net were reflected in carbon isotope discrimination (δ¹³C, p < 0.001) and annual decline in fruit yield (−35%, p < 0.001). Our results demonstrate the suitability of SD as a trait to improve WUE, but also identifies a trade-off between water savings and productivity, which requires consideration for breeding.