Water, nutrient and light deficiency during the co-growth period are the major factors limiting the productivity of the apple–maize alley cropping system in Loess Plateau, China. Therefore, it is crucial to optimize the management of water and fertilizer in the region. The effects of different irrigation and fertilizer levels on photosynthetic characteristics, growth, yield, water consumption (ET) and water use efficiency were studied in a young apple-maize intercropping system during 2014–2016. The treatments included three levels of maximum irrigation, namely 50% (W1), 65% (W2), and 85% (W3) of field capacity (Fc), and three different NPK fertilization levels (289.0-118.0-118.0, 412.4-168.8-168.8 and 537.0-219.0-219.0 kg∙ha−1), which were designated F1, F2 and F3, respectively. In addition, the rain-fed (neither irrigation nor fertilizer) crop was included as the control (CK). The F1 significantly increased the net rate of photosynthesis (Pn) and leaf water-use efficiency (LWUE) of both apple and maize. For maize, the effect of irrigation was greater than that of fertilizers on water use, but smaller on growth indicators and yield. The ET of the alley cropping systems increased with the amount of irrigation but decreased as the dose of fertilizers increased. Growth and yield of maize increased when the amount of irrigation increased, but were inversely related to fertilizer dose. The canopy architecture appeared to be regulated through differential absorption of water and nutrients. The Pn and transpiration (Tr) in maize decreased as the distance from the tree line increased, and the extent of decrease grew over time, suggesting greater interspecific competition. It is recommended that dwarf crops should be planted after intercropping for 5 years according to the change in photosynthetic index with intercropping years under different treatments. Multiple regression analysis indicated the following regime to be optimal during the first 3–5 years of the intercropping in terms of the yield of maize and water use in the alley cropping system: maximum watering (85% Fc) and minimum fertilization (289.0-118.0-118.0 kg ha−1 NPK).
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