Identification and development of molecular markers linked to Phytophthora root rot resistance in pepper (Capsicum annuum L.)

Phytopthora root rot in pepper (C. annuum) is caused by Phytophthora capsici L., which exhibits a high level of pathogenic diversity. Resistance to this disease is conditioned by a number of quantitative trait loci. Pyramiding resistance alleles is desirable and could be simplified by the use of molecular markers tightly linked to the resistance genes. The purpose of this study was development of molecular markers linked to Phytophthora root rot resistance. An F-8 recombinant inbred line (RIL) population derived from a cross between YCM334 and a susceptible cultivar 'Tean' was used in combination with bulk segregant analysis utilizing RAPD and conversion of AFLP markers linked to Phytophtora root rot resistance into sequence-characterized amplified region (SCAR) markers. In conversion: one marker was successfully converted into a co-dominant SCAR marker SA133_4 linked to the trait. In bulked segregant analysis (BSA): three RAPD primers (UBC484, 504, and 553) produced polymorphisms between DNA pools among 400 primers screened. Genetic linkage analysis showed that the SCAR and RAPD markers were located on chromosome 5 of pepper. Quantitative trait locus (QTL) analysis showed that the SA133_4 and UBC553 were linked to Phytophtora root rot resistance. These markers were correctly identified as resistant or susceptible in nine promising commercial pepper varieties. These markers will be beneficial for marker-assisted selection in pepper breeding.