Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposonbased markers

Abstract

Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, includingTurkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversityand population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers.A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entiregermplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescenssubsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content ofthe markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, andprincipal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a fewsubclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level,the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found betweenthe iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing thegenetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serveas a foundation for the development of new and improved pepper varieties.