Genetic characterization of pepper (Capsicum annuum L.) genotypes from central Anatolia with SSR and SCAR markers

The major objective in pepper breeding programs is to generate high yielding novel varieties resistant to pests and diseases, tolerant to abiotic stress conditions with improved fruit quality traits including capsaicin content. Germplasm collections are important sources of variability for breeding studies. Molecular markers are important tools to evaluate genetic relationships among germplasm collections. Moreover, markers are used to select the genotypes conferring the desired traits via marker-assisted selection (MAS) as a powerful approach accelerating breeding programs. In the current study, 56 pepper genotypes selected among 313 pepper genotypes collected from K?r?ehir province in the Central Anatolian region of Turkey according to their agronomic and morphological characteristics were used for molecular assays. Six SSR markers two of which were linked to fruit morphology were selected to characterize pepper genotypes according to their high polymorphism information content. Three SCAR markers associated with capsaicinoid synthesis and resistance to Phytophtora capsici (Phyto.5.2) in pepper were used to assess pungency and resistance among genotypes. According to the results obtained with SSR markers, the total number of alleles ranged from 1 to 8 among genotypes. The most polymorphic SSR markers were CaeMS015 and CAMS452 within the pepper population. The genetic distance among genotypes was determined ranging between 0.75-1.00. The segregation of the SCAR marker BF6-BF8 linked to pungency in pepper was determined relative to pungent and sweet reference cultivars. The OP004.717 SCAR marker linked to Phytophtora capsici was tested among genotypes relative to CM334 pepper variety, known as a source of resistance to Phytophtora.