Breeding for Phytophthora capsici Resistance in Pepper (Capsicum annuum)

A major problem for the pepper (Capsicum annuum) industry is the root and crown rot disease caused by Phytophthora capsici (Pc), to which all commercial varieties suffer yield losses despite good management practices and available landraces with high levels of resistance. Introgression of genetic resistance from pepper landraces to cultivated varieties would benefit the growers and environment through reduced pesticide applications and increased crop value. Genetic linkage maps and a physical genomic map were employed to identify resistance loci and candidate genes conferring resistance. Pepper recombinant inbred lines (RILs) have been systematically screened for Pc resistance against a set of isolates collected from Mexico, New Mexico, New Jersey, California, Michigan and Tennessee. Quantitative Trait Loci (QTL) associated with effective resistance across isolates have been identified and validated with SNP markers across additional segregating populations. RNA-Seq data were also compared in resistant and susceptible bulks to evaluate differential expression leading to resistance. By leveraging transcriptomic and genomic information, we describe several candidate genes responsible for the major QTL on chromosome P5 for resistance toPc. SNP markers for the resistant allele were validated to facilitate gene pyramiding schemes for recurrent selection in pepper.