Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.)

Abstract

Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is known about how common bean plants defend themselves against this fungal pathogen. In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and metabolomic processes in common bean infected with FSP. There were 29,722 differentially regulated genes and 300 differentially regulated metabolites between control and infected plants. The combined omics approach revealed that FSP is perceived by PAMP-triggered immunity and effector-triggered immunity. Infected seedlings showed that common bean responded by cell wall modification, ROS generation, and a synergistic hormone-driven defense response. Further analysis showed that FSP induced energy metabolism, nitrogen mobilization, accumulation of sugars, and arginine and proline metabolism. Importantly, metabolic pathways were most significantly enriched, which resulted in increased levels of metabolites that were involved in the plant defense response. A correspondence between the transcript pattern and metabolite profile was observed in the discussed pathways. The combined omics approach enhances our understanding of the less explored pathosystem and will provide clues for the development of common bean cultivars' resistant to FSP.

Keywords: Fusarium sp; common bean; fungus–plant interactions; induced response; metabolome; transcriptome.

Figure 1

Fusarium solani f. sp. Phaseoli inoculated (FS) and non-inoculated (CK) common bean seedlings at 2, 4, 8, 12, and 18 h post infection.

Figure 2

(a) Distribution of the gene expression in FSP-infected (FS) and non-infected (CK) common bean roots; (b) Pearson correlations between CK and FS replicates; and (c) principle component analysis of expressed genes.

Figure 3

(a) Differential gene volcano map and (b) differential gene cluster heat map; the abscissa represents the sample name and hierarchical clustering results, and the ordinate represents the differential genes and hierarchical clustering results.

Figure 4

Statistics of KEGG enrichment.

Figure 5

qRT-PCR validation of the selected common bean differentially expressed genes in control (CK) and FS (FSP-infected seedlings) 18 h after infection.

Figure 6

Metabolic profile of FSP-infected common bean roots. (a) Major classes of detected metabolites in common bean roots; (b) a heatmap hierarchical clustering of the detected metabolites in FS and CK groups; and (c) the top 10 differentially expressed metabolites.

Figure 7

(a) Joint KEGG enrichment p-value histogram, (b) quadrant diagram representing the association of transcriptomic and metabolomic variation in FS vs. CK; the black dotted lines represent the differential thresholds. Outside the threshold lines, there were significant differences in the gene/metabolites, and within the threshold lines are shown the unchanged gene/metabolites. Each point represents a gene/metabolite. Black dots = unchanged genes/metabolites, green dots = differentially accumulated metabolites with unchanged genes, red dots = differentially expressed genes with unchanged metabolites, and blue dots = both differentially expressed genes and differentially accumulated metabolites. (c) Correlation coefficient cluster heat map (>0.8).