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Background   Phytophthora capsici  root rot (PRR) is a disastrous disease in peppers ( Capsicum spp .) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wilting. Most studies on the QTL mapping of  P. capsici  resistance suggested a consensus broad-spectrum QTL on chromosome 5 named  Pc.5.1  regardless of  P. capsici  isolates and resistant resources. In addition, all these reports proposed NBS-ARC domain genes as candidate genes controlling resistance.    Results  We screened out 10 PRR-resistant resources from 160 Capsicum germplasm and inspected the response of locus  Pc.5.1  and NBS-ARC genes during  P. capsici  infection by comparing the root transcriptomes of resistant pepper 305R and susceptible pepper 372S. To dissect the structure of  Pc.5.1 , we anchored genetic markers onto pepper genomic sequence and made an extended  Pc5.1  ( Ext-Pc5.1 ) located at 8.35Mb38.13Mb on chromosome 5 which covered all  Pc5.1  reported in publications. A total of 571 NBS-ARC genes were mined from the genome of pepper CM334 and 34 genes were significantly affected by  P. capsici  infection in either 305R or 372S. Only 5 inducible NBS-ARC genes had LRR domains and none of them was positioned at Ext -Pc5.1 .  Ext-Pc5.1  did show strong response to  P. capsici  infection and there were a total of 44 differentially expressed genes (DEGs), but no candidate genes proposed by previous publications was included.  Snakin-1  ( SN1 ), a well-known antimicrobial peptide gene located at  Pc5.1 , was significantly decreased in 372S but not in 305R. Moreover, there was an impressive upregulation of sugar pathway genes in 305R, which was confirmed by metabolite analysis of roots. The biological processes of histone methylation, histone phosphorylation, DNA methylation, and nucleosome assembly were strongly activated in 305R but not in 372S, indicating an epigenetic-related defense mechanism.    Conclusions  Those NBS-ARC genes that were suggested to contribute to  Pc5.1  in previous publications did not show any significant response in  P. capsici  infection and there were no significant differences of these genes in transcription levels between 305R and 372S. Other pathogen defense-related genes like  SN1  might account for  Pc5.1 . Our study also proposed the important role of sugar and epigenetic regulation in the defense against  P. capsici .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07705-z.

The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers