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. 2022 Jan 5:12:800535.
doi: 10.3389/fpls.2021.800535. eCollection 2021.

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

Penghui Yang  1 , Yujie Chang  1 , Lanfen Wang  1 , Shumin Wang  1 , Jing Wu  1
Affiliations

Regulatory Mechanisms of the Resistance to Common Bacterial Blight Revealed by Transcriptomic Analysis in Common Bean (Phaseolus vulgaris L.)

Penghui Yang et al. Front Plant Sci. .

Abstract

Common bean blight (CBB), primarily caused by Xanthomonas axonopodis pv. phaseoli (Xap), is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). The tepary bean genotype PI 319443 displays high resistance to Xap, and the common bean genotypes HR45 and Bilu display high resistance and susceptibility to Xap, respectively. To identify candidate genes related to Xap resistance, transcriptomic analysis was performed to compare gene expression levels with Xap inoculation at 0, 24, and 48 h post inoculation (hpi) among the three genotypes. A total of 1,146,009,876 high-quality clean reads were obtained. Differentially expressed gene (DEG) analysis showed that 1,688 DEGs responded to pathogen infection in the three genotypes. Weighted gene coexpression network analysis (WGCNA) was also performed to identify three modules highly correlated with Xap resistance, in which 334 DEGs were likely involved in Xap resistance. By combining differential expression analysis and WGCNA, 139 DEGs were identified as core resistance-responsive genes, including 18 genes encoding resistance (R) proteins, 19 genes belonging to transcription factor families, 63 genes encoding proteins with oxidoreductase activity, and 33 plant hormone signal transduction-related genes, which play important roles in the resistance to pathogen infection. The expression patterns of 20 DEGs were determined by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-seq results.

Keywords: RNA-seq; WGCNA; common bacterial blight; common bean; plant resistance.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Pathogenicity of strain XS2 on PI 319443, HR45, and Bilu. (A) The picture shows the comparison of three genotypes inoculation pathogen for 7 days, and the red arrows indicate the inoculation area on Bilu. (B) Standard curve based on different concentrations of Xanthomonas axonopodis pv. phaseoli strain XS2 DNA with water and three genotypes DNA solution. (C) Xanthomonas axonopodis pv. phaseoli DNA amount in the inoculated leave of three genotypes detected by real time quantitative PCR. Asterisks indicate significantly different at 0.01 probability levels (p < 0.01).
FIGURE 2
FIGURE 2
Different expressed genes in different subgroups. (A) Differential genes up and down regulated after inoculation Xap of PI 319443, HR45 and Bilu. (B) Comparison of differential genes between genotypes. (C) Venn diagrams of DEGs of K/R/S at 0, 24, and 48 h time points after Xap inoculation. (D) Venn diagram of DEGs in response to resistant genotypes. Each box represents genes being up-regulated (red) and down-regulated (blue).
FIGURE 3
FIGURE 3
Functional analysis of 1,688 DEGs. (A) GO enrichment of DEGs. (B) KEGG enrichment of DEGs.
FIGURE 4
FIGURE 4
Weighted gene co-expression network analysis (WGCNA) in resistance to Xap infection. (A) Hierarchical cluster diagram of coexpression modules according to WGCNA. (B) Gene coexpression modules showing the cluster dendrogram (above) and the heatmap for the correlation coefficient between the modules (below). (C) Module–trait relationships. Each cell contains the corresponding correlation and p value.
FIGURE 5
FIGURE 5
Comparison of genes expression levels using RNA-seq and qRT-PCR. K, tepary bean PI 319443; R, resistant genotype HR45; S, susceptible genotype Bilu. 0, 1 and 2 represent 0, 24 and 48 h post inoculation, respectively.
See this image and copyright information in PMC

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