New SNP markers for raspberry germplasm genotyping

Since 2003 more then 250 raspberry (Rubus idaeus) accessions were collected at FEM in order to generate a germplsam collection, which needed to be genotyped. To do so, ten new SNP markers were developed on 10 raspberry varieties, starting from SCAR markers transferred from diploid strawberries and apple (Sargent et al.,2007; Sargent et al., 2009). As results of sequencing analysis, new raspberry sequences of anthocyanidin synthase (ANS), lipoxygenase (LOX), ent‐kaurene oxydase (EKO), cynnamyl alcohol deydrogenase (CAD), exspansin (EXP), dihydroflavonol 4‐reductase (DFR), cytosolic ascorbate peroxidase (APX), spermine synthase (ACL5), alpha amylase (AMY), maltose transporter (MEX), soluble inorganic pyrophosphatase (SIP), polyamine oxidase (PAO), pectate lyase (PL) enzyme regions were obtained and the polymorphisms presence was assessed. Finally, the germplasm genotyping was done on about half of the accessions number using the new markers. The data obtained were analysed with PowerMarker v.3.25, NTSY and STRUCTURE softwares to determine the genetic diversity of the whole collection and to obtain a preliminary cluster analysis. These molecular markers might be helpful not only for germplasm characterization but also, such as candidate genes, for mapping, synteny studies within the Rosaceae family and as a starting point functional to marker‐assisted selection for raspberry breeding programs.