Identification of Key Transcription Factors Related to Bacterial Spot Resistance in Pepper through Regulatory Network Analyses

Abstract

Bacterial spot (BS), caused by Xanthomonas campestris pv. Vesicatoria (Xcv), severely affects the quality and yield of pepper. Thus, breeding new pepper cultivars with enhanced resistance to BS can improve economic benefits for pepper production. Identification of BS resistance genes is an essential step to achieve this goal. However, very few BS resistance genes have been well characterized in pepper so far. In this study, we reanalyzed public multiple time points related to RNA-seq data sets from two pepper cultivars, the Xcv-susceptible cultivar ECW and the Xcv-resistant cultivar VI037601, post Xcv infection. We identified a total of 3568 differentially expressed genes (DEGs) between two cultivars post Xcv infection, which were mainly involved in some biological processes, such as Gene Ontology (GO) terms related to defense response to bacterium, immune system process, and regulation of defense response, etc. Through weighted gene co-expression network analysis (WGCNA), we identified 15 hub (Hub) transcription factor (TF) candidates in response to Xcv infection. We further selected 20 TFs from the gene regulatory network (GRN) potentially involved in Xcv resistance response. Finally, we predicted 4 TFs, C3H (p-coumarate 3-hydroxylase), ERF (ethylene-responsive element binding factor), TALE (three-amino-acid-loop-extension), and HSF (heat shock transcription factor), as key factors responsible for BS disease resistance in pepper. In conclusion, our study provides valuable resources for dissecting the underlying molecular mechanism responsible for Xcv resistance in pepper. Additionally, it also provides valuable references for mining transcriptomic data to identify key candidates for disease resistance in horticulture crops.

TALE Transcription Factors in Sweet Orange (Citrus sinensis): Genome-Wide Identification, Characterization, and Expression in Response to Biotic and Abiotic Stresses

“…In this regard, the findings of a recent study provide evidence to indicate that the Gh BLH7/ Gh OFP complex in cotton functions as a negative regulator in regulating resistance to Verticillium wilt by inhibiting lignin biosynthesis and the JA signaling pathway ( Ma et al, 2020 ). Furthermore, on the basis of regulatory network analyses, TALE family genes have been predicted to be key factors mediating resistance to bacterial spot disease in pepper ( Zhu et al, 2021 ). However, there have been comparatively few studies that have investigated the involvement of CsTALE genes in biotic stress responses, although we assume that their roles in this respect have been underestimated.…”

Characterization of Expression and Epigenetic Features of Core Genes in Common Wheat

“…All networks were visualized using Cytoscape (v3.6.1) software [ 37 ]. Source codes can be found in our previous publication [ 38 ].…”

Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense

“…Weighted gene coexpression network analysis (WGCNA), based on transcriptome data that could identify specific modules and genes related to target traits, was performed by dividing genes with similar expression patterns into the same module ( Langfelder and Horvath 2008 ; Zou et al 2019 ; Ali et al 2020 ; Cheng et al 2020 ). This method has been used to study high-quality fiber in upland cotton, soybean seed set and size, seed development in chickpea, and bacterial spot resistance in pepper in the past 5 years ( Du et al 2017 ; Garg et al 2017 ; Zou et al 2019 ; Feng et al 2021 ; Jiang et al 2021 ; Zhu, Gao, et al 2021 ). The combined analysis of the transcriptome and QTLs can quickly narrow down the range of genes and accurately select genes during key developmental stages ( Khattak et al 2019 ; Wang, Zheng, et al 2020 ; Laoue et al 2021 ; Li et al 2021 ).…”