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

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.

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Comparative Mapping of Three Bacterial, Three Fungal, and One Virus Disease-resistance Genes in Common Bean

HortScience ◽

10.21273/hortsci.33.3.547a ◽

1998 ◽

Vol 33 (3) ◽

pp. 547a-547

Author(s):

Geunhwa Jung ◽

James Nienhuis ◽

Dermot P. Coyne ◽

H.M. Ariyarathne

Keyword(s):

Disease Resistance ◽

Common Bean ◽

Pseudomonas Syringae ◽

Resistance Genes ◽

Fungal Pathogens ◽

Xanthomonas Campestris ◽

Virus Disease ◽

Disease Resistance Genes ◽

Brown Spot ◽

Viral Pathogen

Common bacterial blight (CBB), bacterial brown spot (BBS), and halo blight (HB), incited by the bacterial pathogens Xanthomonas campestris pv. phaseoli (Smith) Dye, Pseodomonas syringae pv. syringa, and Pseudomonas syringae pv. phaseolicola, respectively are important diseases of common bean. In addition three fungal pathogens, web blight (WB) Thanatephorus cucumeris, rust Uromyces appendiculatus, and white mold (WM) Sclerotinia sclerotiorum, are also destructive diseases attacking common bean. Bean common mosaic virus is also one of most major virus disease. Resistance genes (QTLs and major genes) to three bacterial (CBB, BBS, and HB), three fungal (WB, rust, and WM), and one viral pathogen (BCMV) were previously mapped in two common bean populations (BAC 6 × HT 7719 and Belneb RR-1 × A55). The objective of this research was to use an integrated RAPD map of the two populations to compare the positions and effect of resistance QTL in common bean. Results indicate that two chromosomal regions associated with QTL for CBB resistance mapped in both populations. The same chromosomal regions associated with QTL for disease resistance to different pathogens or same pathogens were detected in the integrated population.

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Response of Bell Pepper Cultivars to Bacterial Spot Pathogen Races that Individually Overcome Major Resistance Genes

Plant Disease ◽

10.1094/pdis.1998.82.2.181 ◽

1998 ◽

Vol 82 (2) ◽

pp. 181-186 ◽

Cited By ~ 34

Author(s):

C. S. Kousik ◽

D. F. Ritchie

Keyword(s):

Resistance Genes ◽

Xanthomonas Campestris ◽

Field Experiments ◽

King Arthur ◽

Bacterial Spot ◽

Initial Inoculum ◽

Bell Peppers ◽

Or Gene ◽

Major Resistance Genes ◽

Significant Disease

The effect of major resistance genes (Bs1, Bs2, and Bs3) or gene combinations for resistance to bacterial spot of bell peppers (Xanthomonas campestris pv. vesicatoria) in 15 commercial cultivars on disease reduction and yield were studied during 1995 and 1996. Reaction of cultivars to specific races (races 1, 2, or 3) of the pathogen corresponded with seed company claims for resistance against these races. Races 1 to 4 were used as initial inoculum in 1995, and races 1 to 6 in 1996 field experiments. Cultivars with no known resistance genes to bacterial spot (e.g., Camelot, Jupiter, and Valiant), a single resistance gene (X3R Camelot, King Arthur), or a combination of Bs1 and Bs3 genes (Guardian, Sentinel, and Admiral) were severely diseased. Yields were reduced in all inoculated cultivars compared to non-inoculated cultivars used as controls. Although races 4 and 6 caused significant disease in cultivars with only Bs1 (King Arthur) or Bs2 (X3R Camelot) genes, cultivars with a combination of Bs1 and Bs2 (Boynton Bell, PR9300-8) had much lower levels of bacterial spot. Roger 4178, a hybrid with a combination of Bs1, Bs2, and Bs3 genes, had the lowest disease ratings. Overall, race 3 was predominant during 1995, while races 3 and 6 were recovered most frequently in 1996.

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RsmA Regulates Biofilm Formation in Xanthomonas campestris through a Regulatory Network Involving Cyclic di-GMP and the Clp Transcription Factor

PLoS ONE ◽

10.1371/journal.pone.0052646 ◽

2012 ◽

Vol 7 (12) ◽

pp. e52646 ◽

Cited By ~ 28

Author(s):

Xiu-Hong Lu ◽

Shi-Qi An ◽

Dong-Jie Tang ◽

Yvonne McCarthy ◽

Ji-Liang Tang ◽

...

Keyword(s):

Transcription Factor ◽

Regulatory Network ◽

Biofilm Formation ◽

Xanthomonas Campestris

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Expression and Functional Roles of the Pepper Pathogen–Induced bZIP Transcription Factor CabZIP2 in Enhanced Disease Resistance to Bacterial Pathogen Infection

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-14-0313-r ◽

2015 ◽

Vol 28 (7) ◽

pp. 825-833 ◽

Cited By ~ 27

Author(s):

Chae Woo Lim ◽

Woonhee Baek ◽

Sohee Lim ◽

Sang-Wook Han ◽

Sung Chul Lee

Keyword(s):

Transcription Factor ◽

Disease Resistance ◽

Pseudomonas Syringae ◽

Xanthomonas Campestris ◽

Virulent Strain ◽

Bzip Transcription Factor ◽

Bacterial Disease ◽

Virus Induced Gene Silencing ◽

Pepper Plants

A pepper bZIP transcription factor gene, CabZIP2, was isolated from pepper leaves infected with a virulent strain of Xanthomonas campestris pv. vesicatoria. Transient expression analysis of the CabZIP2-GFP fusion protein in Nicotiana benthamiana revealed that the CabZIP2 protein is localized in the cytoplasm as well as the nucleus. The acidic domain in the N-terminal region of CabZIP2 that is fused to the GAL4 DNA-binding domain is required to activate the transcription of reporter genes in yeast. Transcription of CabZIP2 is induced in pepper plants inoculated with virulent or avirulent strains of X. campestris pv. vesicatoria. The CabZIP2 gene is also induced by defense-related hormones such as salicylic acid, methyl jasmonate, and ethylene. To elucidate the in vivo function of the CabZIP2 gene in plant defense, virus-induced gene silencing in pepper and overexpression in Arabidopsis were used. CabZIP2-silenced pepper plants were susceptible to infection by the virulent strain of X. campestris pv. vesicatoria, which was accompanied by reduced expression of defense-related genes such as CaBPR1 and CaAMP1. CabZIP2 overexpression in transgenic Arabidopsis plants conferred enhanced resistance to Pseudomonas syringae pv. tomato DC3000. Together, these results suggest that CabZIP2 is involved in bacterial disease resistance.

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Regulatory Network Analyses Reveal Genome-Wide Potentiation of LIF Signaling by Glucocorticoids and Define an Innate Cell Defense Response

PLoS Genetics ◽

10.1371/journal.pgen.1000224 ◽

2008 ◽

Vol 4 (10) ◽

pp. e1000224 ◽

Cited By ~ 31

Author(s):

David Langlais ◽

Catherine Couture ◽

Aurélio Balsalobre ◽

Jacques Drouin

Keyword(s):

Defense Response ◽

Regulatory Network ◽

Cell Defense ◽

Network Analyses ◽

Genome Wide

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Rice ESTs with disease-resistance gene- or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs

Molecular Genetics and Genomics ◽

10.1007/s004380000415 ◽

2001 ◽

Vol 265 (2) ◽

pp. 302-310 ◽

Cited By ~ 48

Author(s):

Z. Wang ◽

G. Taramino ◽

D. Yang ◽

G. Liu ◽

S.V. Tingey ◽

...

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Defense Response ◽

Disease Resistance Gene ◽

Response Gene ◽

Major Resistance Genes

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The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes

The Plant Journal ◽

10.1046/j.1365-313x.1999.t01-1-00600.x ◽

1999 ◽

Vol 20 (3) ◽

pp. 265-277 ◽

Cited By ~ 224

Author(s):

Walter Gassmann ◽

Matthew E. Hinsch ◽

Brian J. Staskawicz

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Bacterial Resistance ◽

Disease Resistance Genes

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Construction of transcription factor mutual regulatory network based on a new database

Medical Engineering and Bioinformatics ◽

10.2495/meb140541 ◽

2014 ◽

Author(s):

Zhenping Yang ◽

Wei Wang ◽

Yang Yang ◽

Hongfei Chen ◽

Jinke Wang

Keyword(s):

Transcription Factor ◽

Regulatory Network

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Bereavement or Breakup: A Network Approach to Modeling Differential Pathways into Depression

10.31234/osf.io/38r4j ◽

2019 ◽

Author(s):

Julian Burger ◽

Margaret S. Stroebe ◽

Pasqualina Perrig-Chiello ◽

Henk A.W. Schut ◽

Stefanie Spahni ◽

...

Keyword(s):

Depressive Symptoms ◽

Graphical Models ◽

Contextual Factors ◽

Marital Disruption ◽

Depression Symptoms ◽

Depression Symptom ◽

Multiple Time ◽

Cross Sectional ◽

Network Analyses ◽

Within Subjects

Background: Prior network analyses demonstrated that the death of a loved one potentially precedes specific depression symptoms, primarily loneliness, which in turn links to other depressive symptoms. In this study, we extend prior research by comparing depression symptom network structures following two types of marital disruption: bereavement versus separation. Methods: We fitted two Gaussian Graphical Models to cross-sectional data from a Swiss survey of older persons (145 bereaved, 217 separated, and 362 married controls), and compared symptom levels across bereaved and separated individuals. Results: Separated compared to widowed individuals were more likely to perceive an unfriendly environment and oneself as a failure. Both types of marital disruption were linked primarily to loneliness, from where different relations emerged to other depressive symptoms. Amongst others, loneliness had a stronger connection to perceiving oneself as a failure in separated compared to widowed individuals. Conversely, loneliness had a stronger connection to getting going in widowed individuals. Limitations: Analyses are based on cross-sectional between-subjects data, and conclusions regarding dynamic processes on the within-subjects level remain putative. Further, some of the estimated parameters in the network exhibited overlapping confidence intervals and their order needs to be interpreted with care. Replications should thus aim for studies with multiple time points and larger samples. Conclusions: The findings of this study add to a growing body of literature indicating that depressive symptom patterns depend on contextual factors. If replicated on the within-subjects level, such findings have implications for setting up patient-tailored treatment approaches in dependence of contextual factors.

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