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

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BMC Plant Biology

, 17:84

Plant-biotic interactions


BackgroundRhizoctonia 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.

ResultsTranscriptomics RNAseq and metabolomics 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.

ConclusionsAs 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.

KeywordsGlycine max Bidirectional orthogonal projections to latent structures Primary metabolism Rhizoctonia solani Transcriptomics AbbreviationsH NMRProton nuclear magnetic resonance

3PGA3-phosphoglyceric acid or glycerate-3-phosphate

ADHAlcohol dehydrogenase

AGAnastomosis group

AGPAlpha-glucan phosphorylase

AGTAlanine-glyoxylate transaminase



ASNAsparagine synthetase




cDNAComplementary deoxyribonucleic acid

ChlA-BChlorophyll A-B binding protein

CoACoenzyme A

D2ODeuterium oxide

DEDifferentially expressed


DPSC2Delta-1-pyrroline-5-carboxylate synthase 2



FDHFormate dehydrogenase

FDRFalse discovery rate






GABAGamma-aminobutyric acid




GOGene ontology


h.p.i.Hours post-inoculation

KEGGKyoto encyclopedia of genes and genomes


MLSMalate synthase

O2PLSBidirectional orthogonal projections to latent structures

PALPhenylalanine ammonia lyase

PCAPrinciple component analysis

PDAPotato dextrose agar


PEPCPhosphoenolpyruvate carboxykinase 1



PLS-DAPartial least squares-discriminant analysis

PR4Pathogenesis-related protein 4

PRESSPrediction error sum of squares


PSIIPhotosystem II

QcumCumulated predictive power

QCQuality control

qRT-PCRQuantitative real-time polymerase chain reaction

RX, RYFraction of the sum of squares for all X and Y variables, respectively

RFBRhizoctonia foliar blight

RNAseqRNA sequencing

ROSReactive oxygen species


SRAShort reads archive



TCATricarboxylic acid

THIThiamine biosynthesis



UKN2Hypothetical protein unknown 2

VIPVariable importance

WtWild type

Electronic supplementary materialThe online version of this article doi:10.1186-s12870-017-1020-8 contains supplementary material, which is available to authorized users.

Author: Tanya R. Copley - Konstantinos A. Aliferis - Daniel J. Kliebenstein - Suha H. Jabaji


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