Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana

A Novel Endophytic Fungus Fusarium falciforme R-423 for the Control of Rhizoctonia solani Root Rot in Pigeon Pea as Reflected by the Alleviation of Reactive Oxygen Species-Mediated Host Defense Responses

Rhizoctonia solani root rot is a devastating fungal disease that causes significant yield losses in legume crops. A novel endophytic fungus Fusarium falciforme R-423 isolated from pigeon pea had a significant antagonistic capacity against R. solani. F. falciforme R-423 extracts could inhibit R. solani growth and cause it to die. Four host-specific and 15 genus-specific metabolites were identified as potential antimicrobial compounds. F. falciforme R-423's inoculation effectively controlled R. solani root rot in pigeon pea seedlings and promoted root growth. Co-inoculation of F. falciforme R-423 and R. solani reduced the levels of oxidative stress, pathogenesis- and biosynthesis-related gene expression, and phenolic compound accumulation in roots compared to those infected with R. solani, confirming that reactive oxygen species-mediated host defense responses were alleviated due to the effective control of R. solani by F. falciforme R-423. Overall, F. falciforme R-423 was a promising biocontrol agent against R. solani root rot in legume crops.

DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana

Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible), in response to P. sansomeana at two time points: 4 and 16 hours post-inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines.