Summary: Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions.
Overall Design: Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.
Inoculum for both isolates was grown for seven days on potato dextrose agar (PDA) at 25 °C with a 12-h photoperiod. Conidia were collected by rinsing plates with sterile water, scraping the agar surface with a scalpel and filtering the conidial suspension through sterile cloth. Spore suspension was adjusted to a final concentration of 1 × 106 conidia/ml based on microscopic counts using a Bürker chamber. Fifteen seeds of the partially resistant Forrest genotype were placed on a paper towel moistened with sterile distilled water and inoculated by pipette with 100 μl of 1 × 106 conidial suspension of FO36 or FO40 isolates. Another moistened paper towel was placed over the inoculated seeds, rolled up, and placed vertically in a 25-l bucket. An open plastic bag was placed over each towel to avoid cross-contamination between isolates. A black plastic bag was placed over each bucket and they were placed on a bench at room temperature (~22 °C). Noninoculated checks were included to ensure that other seed pathogens were not present. For RNA-Seq analysis, roots were collected at 72 and 96 hpi. Noninoculated control roots were sampled at the same times listed above. Three pools of five roots were prepared for each isolate and sampling time. The resulting samples were immediately frozen in liquid nitrogen and stored at -80 °C until biological analysis were carried out.
Treatment Protocol:
Soybean [G. max (L.) Merrill] partially resistant genotype Forrest was evaluated after inoculation with a conidial suspension of non-pathogenic FO36 and pathogenic FO40 F. oxysporum isolates.
Extract Protocol:
Soybean seedlings were collected, flash frozen on liquid nitrogen, and RNA was extracted using Trizol reagent.
Library Construction Protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing
Molecule Type:
-
Library Source:
Library Layout:
PAIRED
Library Strand:
-
Platform:
ILLUMINA
Instrument Model:
Illumina HiSeq 2500
Strand-Specific:
Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource
GEN Sample ID
GEN Dataset ID
Project ID
BioProject ID
Sample ID
Sample Name
BioSample ID
Sample Accession
Experiment Accession
Release Date
Submission Date
Update Date
Species
Race
Ethnicity
Age
Age Unit
Gender
Source Name
Tissue
Cell Type
Cell Subtype
Cell Line
Disease
Disease State
Development Stage
Mutation
Phenotype
Case Detail
Control Detail
Growth Protocol
Treatment Protocol
Extract Protocol
Library Construction Protocol
Molecule Type
Library Layout
Strand-Specific
Library Strand
Spike-In
Strategy
Platform
Instrument Model
Cell Number
Reads Number
Gbases
AvgSpotLen1
AvgSpotLen2
Uniq Mapping Rate
Multiple Mapping Rate
Coverage Rate
Publications
Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum.
