Genetic dissection of Phytophthora capsici resistance in Capsicum annuum by genome-wide association mapping and fine mapping

Phytophthora capsici Leonian is a destructive pathogen that affects pepper production worldwide. Resistance breeding has been proposed as the most efficient and eco-friendly management strategy for controlling this pathogen. This study aimed to characterize the genetic architecture of P. capsici resistance in pepper to support its resistance breeding. In this study, a panel of 220 accessions of Capsicum annuum were evaluated for resistance to P. capsici under controlled conditions. The panel was genotyped via genotyping-by-sequencing (GBS), and the resulting 955 772 high-quality variations were used for the population stratification analysis and the identification of chromosome regions associated with resistance against P. capsici. Strong association signals were detected mainly on chromosomes 5 (CaRPc5.1) and 10 (CaRPc10.1). The associated single nucleotide polymorphisms (SNPs) explained 5.61–11.71 % of the phenotypic variation. The 220 accessions were divided into four genetic clusters, including an ancestral cluster, a transition cluster, and two recently emerged clusters. P. capsici resistance of the four clusters unveiled compromised resistance to P. capsici during modern domestication, which was hypothesized to be a trade-off for desirable horticultural traits. Using bulked sergeant analysis (BSA) and whole-genome resequencing (WGR), a major locus in an F4:5 population, derived from a cross between the P. capsici-resistant parent A204 and the susceptible parent A198, was mapped to a 1.81 Mb region on chromosome 10, which coincided with the CaRPc10.1 locus. This locus was further fine-mapped into a 32.36 kb region based on two derived F5:6 populations consisting of 2 713 individuals. The Capann_59Chr10g029350 gene, a likely allelic variation of the Pvr4 gene in this interval, was proposed as a strong candidate gene for Phytophthora capsisi resistance. Our results provide molecular perspectives into the P. capsici-resistance mechanism and molecular markers for the improvement of P. capsici resistance in pepper and pave the way for cloning the resistance gene underlying CaRPc10.1.