Synergistically micronutrient co-application improves nutritional quality and effectively reduces aflatoxin contamination in Brassica rapa L. roots.

Aflatoxin B1 (AFB1) contamination and micronutrient deficiencies pose a major challenge to food safety and nutritional security. This study elucidated the synergistic potential of boron (B) and zinc (Zn) co-application to fortify nutritional quality and mitigate AFB1 accumulation in turnip (Brassica rapa L) roots. Seeds were cultivated in soils amended with individual or combined B and Zn at concentrations of 10–25 mg kg− 1. In results, individual B supplementation at 20 mg kg− 1 optimized protein content (10.9%), and the B-Zn interactome provided superior overall metabolic performance. B-Zn synergy significantly enhanced physiological resilience. Specifically, the combined application at 15–20 mg kg− 1 consistently achieved the highest STI and GMP productivity across biochemical traits. Carbohydrate partitioning was significantly improved, with NFE reaching 74.1% at 20 mg kg− 1 of B + Zn. AFB1 toxicity was suppressed by 60.08% at 15 mg kg− 1. RPI of dry matter, protein, and phenolic were consistently positive at 15–20 mg kg− 1 of B + Zn. Co-application enhanced the YSI for NFE, protein, and ash content. PCA confirmed that the synergistic effects of B + Zn treatment provided superior nutritional results compared to individual micronutrient applications. These findings demonstrate that balanced B-Zn supplementation strengthens nutritional composition quality and suppresses AFB1 contamination, supporting the biofortification paradigm as a reproducible strategy for sustainable food quality and crop improvement.