Characterization of pepper accessions using molecular markers linked to pungency and SSR

Peppers of the genus Capsicum are of great socioeconomic importance, being pungency trait their main attraction. Pungency characterization, genetic distance estimates and population structure analysis of the accessions belonging to germplasm banks are important for parent selection which allows to obtain superior progenies. Therefore, the aims of this study were: i) evaluate 81 accessions of the Capsicum spp. Germplasm Bank of Universidade Federal de Sao Carlos (BGC-UFSCar) with molecular markers linked to pungency; ii) estimate the genetic diversity among accessions of the BGC-UFSCar using microsatellite markers (SSR); and iii) evaluate the efficiency of these markers in the distinction among species of Capsicum spp. We noticed that pun1(1) and SNP molecular markers were efficient in predicting the pungent phenotype of BGC-UFSCar accessions in 84.85% and 95.59%, respectively. From a total of 13 amplified microsatellite markers, seven were polymorphic and efficient to discriminate species of Capsicum genus, both through genetic diversity analysis and population structure analysis, which showed three subpopulations. The molecular markers used in this study are useful tools for breeding programs since they were able to characterize and discriminate Capsicum spp. species at DNA level. Information obtained with molecular markers can assist in the selection of contrasting parents for future breeding programs.