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Background  Plant transcription factors (TFs) are key transcriptional regulators to manipulate the regulatory network of host immunity. However, the globally transcriptional reprogramming of plant TF families in response to pathogens, especially between the resistant and susceptible host plants, remains largely unknown.    Results  Here, we performed time-series RNA-seq from a resistant pepper line CM334 and a susceptible pepper line EC01 upon challenged with  Phytophthora capsici , and enrichment analysis indicated that WRKY family most significantly enriched in both CM334 and EC01. Interestingly, we found that nearly half of the WRKY family members were significantly up-regulated, whereas none of them were down-regulated in the two lines. These induced WRKY genes were greatly overlapped between CM334 and EC01. More strikingly, most of these induced WRKY genes were expressed in time-order patterns, and could be mainly divided into three subgroups: early response (3 h-up), mid response (24 h-up) and mid-late response (ML-up) genes. Moreover, it was found that the responses of these ML-up genes were several hours delayed in EC01. Furthermore, a total of 19 induced WRKY genes were selected for functional identification by virus-induced gene silencing. The result revealed that silencing of  CaWRKY03–6 ,  CaWRKY03–7 ,  CaWRKY06–5  or  CaWRKY10–4  significantly increase the susceptibility to  P. capsici  both in CM334 and EC01, indicating that they might contribute to pepper’s basal defense against  P. capsici ; while silencing of  CaWRKY08–4  and  CaWRKY01–10  significantly impaired the disease resistance in CM334 but not in EC01, suggesting that these two WRKY genes are prominent modulators specifically in the resistant pepper plants.    Conclusions  These results considerably extend our understanding of WRKY gene family in pepper’s resistance against  P. capsici  and provide potential applications for genetic improvement against phytophthora blight.

The transcriptional reprograming and functional identification of WRKY family members in pepper’s response to Phytophthora capsici infection