Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages

Sclerotinia stem rot, also referred to as white mold, poses a threat to soybean production world-wide. The causal agent, Sclerotinia sclerotiorum (Lib.) de Bary, can survive in harsh environments and has an extremely broad host range. No naturally complete resistance has been reported to exist in soybean, which makes it a compelling problem. Studying the molecular interactions between soybean and S. sclerotiorum is a promising approach to identify the soybeans genes that are controlling the quantitative resistance and, on the other hand, to discover pathogenicity and virulence factors in S. sclerotiorum which could be considered as targets to disable and weaken the aggressiveness of the pathogen. This study utilized RNA-sequencing to characterize the transcriptomes of the leaves of a susceptible soybean line (AC) and an AC transgenic line (OxO) which contains an enzyme that degrades the oxalic acid (OA) produced by S. sclerotiorum thereby conferring resistance. The leaves were infected with S. sclerotiorum and samples were collected at 4 and 8 hours post inoculation (hpi) to characterize this interaction and to examine the key determinants of resistance and infection at these early infection stages. More than 600 soybean genes were detected with a fairly stringent cutoff as being significantly differentially expressed in response to S. sclerotiorum inoculation. Functional annotations and categorizations revealed that a large percentage of differentially expressed genes (DEGs) were annotated as kinases and transcription factors, depicting a complex network of signal transduction and gene regulation during the initiation of defense responses. Gene Ontology (GO) enrichment analysis demonstrated that host oxidative burst, jasmonic acid and ethylene signaling pathways, and biosynthetic pathways of several soybean anti-microbial secondary metabolites, were all quickly induced in this defense response. Our data also suggested that abscisic acid signaling was highly responsive to S. sclerotiorum infection, and that salicylic acid signaling might be largely inhibited. Interestingly, a potential interplay of a hypersensitive response-like programmed cell death (PCD) and autophagy was detected as a common reaction in both genotypes. It is speculated that, because S. sclerotiorum is a necrotrophic fungus that feeds on dead host cells, inhibiting host cell death could slow down its infection. Our expression data also identified six membrane trafficking-related genes that were proposed to contribute to negative regulation of PCD via suppressing the salicylic acid signaling pathway. Although no statistically significant differences between the two genotypes were due to fungal infection, the quantitative differences between them were discussed. Although apparently minor at these early time points, these quantitative differences could be reflective of defense-related processes that were more intense in OxO. This transcriptomic study also compared the gene expression of the pathogen, S. sclerotiorum, in infected leaves from AC and OxO to that of growth in liquid axenic culture. The comparison revealed dramatic differential transcriptomic responses at 4 and 8 hpi (with close to three thousand genes detected as significantly differentially expressed in leaves versus in culture), revealing a broad range of molecular weapons for S. sclerotiorum to assault its host. Plant cell wall degrading enzymes (PCWDEs) were shown to be one of the major players in the early infection stages and the expression patterns suggested more important roles of pectinases and cutinases for soybean infection at these early time points. Looking at potential fungal effectors, 160 secretory proteins were predicted as candidates. When evaluating the effects of OxO degradation of oxalic acid on S. sclerotiorum gene expression, only three genes were showing statistical significance. However, many genes exhibited quantitative differences such as a higher expression of oxalic acid biosynthetic genes, and genes associated with botcinic acid biosynthesis and numerous PCWDEs. A potential transcriptional crosstalk between oxalic acid and the other virulence factors was hypothesized. Validation of 91 soybean gene expression patterns detected by RNA-Seq was performed by a Fluidigm microfluidic array-based qRT-PCR. This experiment verified the high inductions of about 50 genes from early time points 4 and 8 hpi to later time points at 12 and 24 hpi, supporting the RNA-Seq data. The expression patterns were also consistent with the inoculation using another soybean genotype, William 82. Moreover, the transcriptional responses to oxalic acid solution in about 70 genes were very similar to those in response to infection by S. sclerotiorum, supportive of the role of OA as a major virulence factor of S. sclerotiorum. Several genes displaying interesting expression patterns were discussed; for example, a tonoplast dicarboxylate transporter that could be involved in the maintenance of cellular pH homeostasis was only induced in OxO but suppressed by other treatment with the presence of high levels of oxalic acid. Most of the genes annotated as membrane trafficking components were largely induced at all time points but did not show obvious differences between AC and OxO in qRT-PCR. Moreover, the occurrence of autophagy that could be inhibited by oxalic acid was not clearly detected in any treatments