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

Abstract

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.