Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper

Phytophthora capsici causes devastating disease on many crop species, including Capsicum. Resistance in Capsicum annuum is genetically and physiologically complex. A panel of Capsicum germplasm that included genotypes from both C. annuum and C. chinense showing highly resistant, highly susceptible and intermediate or tolerant responses to the pathogen, respectively, was screened with a series of randomly amplified polymorphic sequence primers to determine which genomic regions contribute to the highest level of resistance. One primer, OpD04, amplified a single band only in those C. annuum and C. chinense genotypes showing the highest level of resistance. The amplified product was cloned, sequenced and used to design longer primers in order to generate a sequence characterized amplified region marker which was then mapped in a reference mapping population and a screened population segregating for resistance to P. capsici. These primers were observed to define a locus on pepper chromosome 5 tightly linked to Phyto.5.2, one of six quantitative trait loci (QTL) previously reported to contribute to P. capsici resistance. These results indicate that the Phyto.5.2 QTL may be widely distributed in highly resistant germplasm and provide improved resolution for this QTL. This work also defines the first breeding tools for this system, allowing for the rapid selection of genotypes likely to be highly resistant to P. capsici.