Transcriptome Profiling Reveals Molecular Players in Early Soybean–Sclerotinia sclerotiorum Interaction

Sclerotinia sclerotiorum causes Sclerotinia stem rot on soybean. Using RNA sequencing, the transcriptomes of the soybean host and the S. sclerotiorum pathogen were simultaneously determined at 4 and 8 h postinoculation (hpi). Two soybean genotypes were involved: a resistant oxalate oxidase (OxO)-transgenic line and its susceptible parent, AC Colibri (AC). Of the 594 genes that were significantly induced by S. sclerotiorum, both hosts expressed genes related to jasmonic acid, ethylene, oxidative burst, and phenylpropanoids. In all, 36% of the differentially expressed genes encoded genes associated with transcription factors, ubiquitination, or general signaling transduction such as receptor-like kinases, mitogen-activated protein kinase kinases, and hormones. No significant differentially expressed genes were identified between genotypes, suggesting that oxalic acid (OA) did not play a differential role in early disease development or primary lesion formation under the conditions used. Looking at pathogen behavior through its gene expression during infection, thousands of genes in S. sclerotiorum were induced at 8 hpi, compared with expression in culture. Many plant cell-wall-degrading enzymes (PCWDEs), sugar transport genes, and genes involved in secondary metabolism were upregulated and could contribute to early pathogenesis. When infecting the OxO plants, there was a higher induction of genes encoding OA, botcinic acid, PCWDEs, proteases, and potential effectors, revealing the wealth of virulence factors available to this pathogen as it attempts to colonize a host. Data presented identify hundreds of genes associated with the very early stages of infection for both the host and pathogen.