The accessibility and use of natural genetic variability in crops is essential for the management of genetic resources and the establishment of innovative breeding programs. Nuclear whole-genome sequences of several cultivated and wild peppers have been recently generated in order to provide crucial information on the evolution, domestication and divergence of pepper species (Capsicum spp.). Despite next generation sequencing (NGS) technologies providing a significant advance in generation of high throughput data, the analysis of a large-scale data and of individuals is still a challenging task. An alternative strategy to Whole Genome Sequencing is to generate a reduced representation of the genome using target enrichment strategies. Among them, genotyping-by-sequencing (GBS) provides a rapid, highly informative, cost-effective tool for exploring genetic diversity on a genome-wide scale. We applied GBS for SNP marker discovery in nuclear genomes and population structure analysis in a collection of cultivated and domesticated peppers. Information generated in this study represents a first step towards future genome-wide association mapping studies and marker-assisted selection programs. In addition, results from this analysis can be used to gain a better understanding of the genetic relationships within the Capsicum genus. In order to provide a further contribution to that issue, we also determined the complete chloroplast DNA (cpDNA) sequence of 11 Capsicum accessions for a total of 8 species generally included in the C. annuum (7), C. baccatum (3) or C. pubescens/eximium complex (1). We performed comparative analysis and identified potential molecular markers able to discriminate among Capsicum species.
