Brassinolide Application Mitigates Blossom-End Rot in Tomato by Enhancing Calcium Homeostasis and Antioxidant Defense Under Calcium Deficiency

Blossom-end rot (BER) in tomatoes is a physiological disorder primarily caused by the disruption of calcium absorption and transport. This study cultivated tomatoes using a trough-based vermiculite system. Two treatments were established: a calcium-deficient nutrient solution and a calcium-deficient nutrient solution supplemented with 0.1 mg/L BR (n = 40 plants per treatment). The activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), as well as the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2), were measured in the leaves. Calcium ion content was also determined in various plant parts. Statistical analysis of differences was performed using Duncan’s multiple range test at a significance level of p < 0.01. Concurrently, transcriptome sequencing of root, stem, and leaf tissues was conducted via high-throughput sequencing technology. The results showed that foliar application of BR under calcium deficiency significantly reduced the incidence of BER (from 26.67% to 6.67%) and effectively increased calcium ion content in leaves, stems, and roots. At the physiological level, BR treatment markedly enhanced the activities of CAT, POD, and SOD in leaves (by 105.70%, 117.12%, and 82.77%, respectively), while reducing H2O2 and MDA contents (by 36.90% and 16.38%, respectively). This indicates that BR alleviates membrane lipid peroxidation damage by enhancing the antioxidant defense system. Gene Ontology (GO) enrichment analysis revealed that the differentially expressed genes (DEGs) were primarily involved in biological processes, such as secondary metabolic processes, response to oxygen-containing compounds, and cell wall organization. KEGG pathway analysis further indicated significant enrichment in pathways, including phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction. Additionally, key genes, such as the cytochrome c oxidase (COX) gene (Solyc03g013460.1), exhibited a gradient up-regulation pattern (root > stem > leaf) in the oxidative phosphorylation pathway. In conclusion, BR likely enhances tomato tolerance to calcium deficiency stress and effectively reduces BER incidence through multiple pathways: regulating calcium absorption and distribution, activating the antioxidant system, modulating hormone signaling pathways, and enhancing energy metabolism. These findings provide a theoretical basis for the application of BR in agricultural production.