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

Qingquan Zhu,Wenli Zhang,Shenghua Gao

doi:10.3390/genes12091351

Qingquan Zhu, Wenli Zhang + Show 1 more

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https://doi.org/10.3390/genes12091351

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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.

Highlights

Pepper (Capsicum annuum L.) is an important vegetable crop for our daily consumption around the world
To investigate the dynamic changes of gene transcription responding to Xanthomonas campestris pv. Vesicatoria (Xcv) infection between the susceptible pepper cultivar early Calwonder (ECW) and the resistant pepper cultivar VI037601, we extracted 18 RNA-seq samples and performed principal component analysis (PCA) by the FPKM expression
We identified a total of 3568 differentially expressed genes (DEGs) in VI037601 relative to ECW at the same time point post Xcv infection (Figure 1B)

Summary

Introduction

Pepper (Capsicum annuum L.) is an important vegetable crop for our daily consumption around the world. It is rich in various nutrients beneficial to human health such as capsaicin, carotenoids, and vitamin C [1]. The production of pepper is always affected by various biotic stresses such as bacterial spot, powdery mildew, and bacterial wilt [3], and abiotic stresses such as low temperature and drought [4,5]. Among these stresses, pepper bacterial spot (BS) disease, caused by Xanthomonas campestris pv. Vesicatoria (Xcv), is one of the most common bacterial diseases for pepper culture and is harmful to the yield and quality of pepper [6], resulting in huge economic losses to the producers

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