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The successful exploitation of germplasm banks, harbouring plant genetic resources indispensable for plant breeding, will depend on our ability to characterize their genetic diversity. The Vegetable Germplasm Bank of Zaragoza (BGHZ) (Spain) holds an important  Capsicum annuum  collection, where most of the Spanish pepper variability is represented, as well as several accessions of other domesticated and non-domesticated  Capsicum  spp from all over the five continents. In the present work, a total of 51  C. annuum  landraces (mainly from Spain) and 51 accessions from nine  Capsicum  species maintained at the BGHZ were evaluated using 39 microsatellite (SSR) markers spanning the whole genome. The 39 polymorphic markers allowed the detection of 381 alleles, with an average of 9.8 alleles per locus. A sizeable proportion of alleles (41.2%) were recorded as specific alleles and the majority of these were present at very low frequencies (rare alleles). Multivariate and model-based analyses partitioned the collection in seven clusters comprising the ten different  Capsicum  spp analysed:  C. annuum ,  C. chinense ,  C. frutescens ,  C. pubescens ,  C. bacatum ,  C. chacoense  and  C. eximium . The data clearly showed the close relationships between  C. chinense  and  C. frutescens .  C. cardenasii  and  C. eximium  were indistinguishable as a single, morphologically variable species. Moreover,  C. chacoense  was placed between  C. baccatum  and  C. pubescens  complexes. The  C. annuum  group was structured into three main clusters, mostly according to the pepper fruit shape, size and potential pungency. Results suggest that the diversification of  C. annuum  in Spain may occur from a rather limited gene pool, still represented by few landraces with ancestral traits. This ancient population would suffer from local selection at the distinct geographical regions of Spain, giving way to pungent and elongated fruited peppers in the South and Center, while sweet blocky and triangular types in Northern Spain.

New Insights into Capsicum spp Relatedness and the Diversification Process of Capsicum annuum in Spain