Candidate Locus Associated with the Inhibitor of Phytophthora capsici Resistance (Ipcr) Gene Linked to Susceptibility in Pepper

Abstract

Phytophthora capsici is a destructive pathogen of pepper ( Capsicum annuum L.), causing severe yield losses worldwide. Although resistance loci derived from the C. annuum landrace CM334 have been widely deployed, durable resistance remains elusive due to complex inheritance and the reported Inhibitor of P. capsici resistance ( Ipcr ) gene that suppresses resistance. We investigated the inheritance and genomic location of Ipcr using an F 2 population derived from a hybridization between CM334 and NMCA10399. Disease evaluations with a virulent P. capsici isolate revealed segregation did not deviate from a 3:13 ratio, consistent with dominant suppression epistasis. Bulk segregant analysis with quantitative trait loci sequencing identified a major susceptibility-associated interval on chromosome 3 (107.6 to 113.4 Mb) significantly associated with susceptibility, in which ΔSNP index values reached –0.62 and G′ statistics exceeded significance thresholds, consistent with dominant suppression of resistance. Candidate gene analysis within this region revealed loci with potential roles in defense regulation, including a CLAVATA3/ESR-related protein, calmodulin-binding protein 60, ASC1-like protein, MLO-like gene, and PBS1-like kinase. These findings refine the genomic position of Ipcr and highlight candidate genes that may condition susceptibility, providing valuable targets for functional validation and breeding strategies to eliminate suppressive alleles and develop durable resistance to P. capsici in pepper.