Comparative transcriptome and co-expression network analysis uncovers the regulatory mechanism of silicon-induced soybean defense against charcoal rot disease

Soybean (Glycine max L.) is highly susceptible to charcoal rot caused by the soil-borne pathogen Macrophomina phaseolina, which can reduce yields by up to 70 %. Effective control methods are lacking, and information on managing the disease is limited. This study investigates how potassium silicate (1.7 mM K2SiO3) enhances soybean resistance to charcoal rot. The treatment significantly improved plant health, reducing the mortality rate of the susceptible genotype TAMS-38 from 69.7 % to 9 %. RNA sequencing revealed 3106 differentially expressed genes linked to disease resistance. Resistant genotypes showed upregulation of genes involved in key defense pathways, enhancing resistance mechanisms against charcoal rot including Pathogenesis-Related Protein 1 (PR1) for Systemic Acquired Resistance (SAR) and Salicylic Acid (SA) pathway, Stress-induced protein H4 for Heat Shock Protein (HSP) Pathway, disease resistance proteins for Resistance gene and Mitogen-Activated Protein Kinase (MAPK) pathways, pleiotropic drug resistance proteins for detoxification, basic secretory protein (BSP) domain for cell wall reinforcement, NRT1/PTR FAMILY 2.13 for nutrient management, receptor-like kinases for pathogen detection, Pruav 1 for resistance, Dehydration responsive element-binding protein 3 (DREB3) for abscisic acid (ABA) signalling in drought, and chitinase class I precursor for fungal cell wall breakdown. A total of 41 key differentially regulated genes were identified, with 8 validated by qRT-PCR, showing potential for genetic improvement and breeding. These findings provide a basis for developing strategies to combat charcoal rot and improve soybean resilience against Macrophomina phaseolina.