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Background    Rhizoctonia solani  AG1-IA is a devastating phytopathogen causing Rhizoctonia foliar blight (RFB) of soybean worldwide with yield losses reaching 60%. Plant defense mechanisms are complex and information from different metabolic pathways is required to thoroughly understand plant defense regulation and function. Combining information from different “omics” levels such as transcriptomics, metabolomics, and proteomics is required to gain insights into plant metabolism and its regulation. As such, we studied fluctuations in soybean metabolism in response to  R. solani  infection at early and late disease stages using an integrated transcriptomics-metabolomics approach, focusing on the regulation of soybean primary metabolism and oxidative stress tolerance.    Results  Transcriptomics (RNAseq) and metabolomics ( 1 H NMR) data were analyzed individually and by integration using bidirectional orthogonal projections to latent structures (O2PLS) to reveal possible links between the metabolome and transcriptome during early and late infection stages. O2PLS analysis detected 516 significant transcripts, double that reported in the univariate analysis, and more significant metabolites than detected in partial least squares discriminant analysis. Strong separation of treatments based on integration of the metabolomes and transcriptomes of the analyzed soybean leaves was revealed, similar trends as those seen in analyses done on individual datasets, validating the integration method being applied. Strong fluctuations of soybean primary metabolism occurred in glycolysis, the TCA cycle, photosynthesis and photosynthates in response to  R. solani  infection. Data were validated using quantitative real-time PCR on a set of specific markers as well as randomly selected genes. Significant increases in transcript and metabolite levels involved in redox reactions and ROS signaling, such as peroxidases, thiamine, tocopherol, proline, L-alanine and GABA were also recorded. Levels of ethanol increased 24 h post-infection in soybean leaves, and alcohol dehydrogenase ( ADH ) loss-of-function mutants of  Arabidopsis thaliana  had higher necrosis than wild type plants.    Conclusions  As a proof-of-concept, this study offers novel insights into the biological correlations and identification of candidate genes and metabolites that can be used in soybean breeding for resistance to  R. solani  AG1-IA infection. Additionally, these findings imply that alcohol and its associated gene product  ADH  may have important roles in plant resistance to  R. solani  AG1-IA causing foliar blight.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-017-1020-8) contains supplementary material, which is available to authorized users.

An integrated RNAseq-1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease