Coordinating source-sink dynamics and canopy photosynthesis through organic fertilizer substitution synergistically enhances foxtail millet yield and quality.

Replacing chemical nitrogen (N) fertilizer with organic fertilizer is widely considered an effective approach to sustain and enhance crop yields under reduced chemical fertilizer inputs. However, the underlying physiological mechanisms remain unclear. This study quantified source-sink growth dynamics and canopy photosynthetic traits in foxtail millet (Setaria italica L.) under varying N reduction ratios (15%, N-15; 30%, N-30) and organic substitution ratios (15%, N+15org; 30%, N+30org) relative to conventional N application (CT, 150 kg ha-1). The results indicated that moderate N fertilizer reduction (15%) exerted no significant adverse effects on grain yield or quality. However, compared with the CT treatment, the N-30 treatment significantly decreased panicle weight and total grain yield by 5.6-8.9% and 9.5-11.2%, the contents of yellow pigment, starch, and protein were lowered by 15.4-30.1%, 2.7-3.6%, and 5.7-9.2%, source and sink activities were significantly suppressed by 21.9-27.3% and 6.1-14.1%, respectively (p < 0.05). Conversely, replacing 30% of chemical N with organic fertilizer (N+30org) significantly increased grain yield by 17.3-23.5%, grain protein content by 6.6-12.2%, and the amylopectin/amylose ratio by 7.5-17.9% relative to CT (p < 0.05). The N+30org treatment enhanced the leaf area index (LAI, 7.0-11.3%), net photosynthetic rate (Pn, 10.6-21.2%), transpiration rate (Tr, 12.1-24.4%), stomatal conductance (Gs, 9.6-16.4%), and the actual quantum efficiency of PSII (ΦPSII, 13.2-15.7%) during the late grain-filling stage (30-40 days after anthesis). Concurrently, the time required to reach peak sink activity (tm,o) was prolonged by 6-11 days by the organic substitution strategy, which also boosted both source and sink activities, expanded the maximum sink biomass (Wmax,h) by 9.8-15.7%, and increased the sink-to-source ratio by 8.7-11.4%. Random Forest importance assessment and partial least squares path modeling (PLS-PM) revealed that grain yield formation was closely associated with sink and source relationships, whereas canopy photosynthetic characteristics may contribute to grain quality. Substituting 30% of chemical N with organic fertilizer was associated with a slower decline in canopy photosynthetic performance and mitigated source supply limitations induced by N fertilizer reduction. Consequently, high photosynthetic capacity during the late grain-filling stage was maintained, and source-sink capacity and activity were substantially enhanced, thereby achieving a synergistic optimization of high yield and superior quality in foxtail millet.