Molecular characterization of Greek pepper (Capsicum annuum L) landraces with neutral (ISSR) and gene-based (SCoT and EST-SSR) molecular markers

•Greek pepper germplasm genotyping.•Use of ISSR, SCoT and EST-SSR in pepper landraces.•Genebank molecular characterization.•HRM analysis of gene-based markers.•SCoT markers an effective marker system for evaluation of pepper genetic diversity.

Thirty landraces were selected from a Gene Bank collection comprising of pepper (Capsicum annuum L.) landraces from across Greece. The genetic variability among the 30 landraces and one commercial greek cultivar, intended for industrial use, was assessed by Inter-Simple Sequence Repeat (ISSR), Start Codon Targeted (SCoT) and Expressed Sequence Tag (EST) - Simple Sequence Repeat (SSR) molecular markers. All genotypes were clearly distinguished in the dendrograms produced, with the ISSR and SCoT dendrograms being the most consistent. Three landraces were grouped together in all dendrogams revealing a possible phylogenetic relationship. Furthermore, EST-SSR markers were combined with High Resolution Melting (HRM) analysis by which the more adequate and confident separation of the landraces was accomplished due to the unique HRM profiles produced. Genotyping the rich Greek pepper germplasm by molecular markers will aid the breeding process towards well adopted Greek pepper cultivars of higher quality and productivity.