Development of a multiplexed microsatellite set for fingerprinting red raspberry (Rubus idaeus) germplasm and its transferability to other Rubus species

This study aimed to develop a standardised and cost effective protocol for fingerprinting red raspberry germplasm using microsatellite (SSR) markers. Twenty SSRs well distributed through the raspberry genome were screened on 16 genetically diverse cultivars to assess polymorphism, allele size range, quality of amplification, ease of scoring, and discriminating power (DF). We selected published SSR markers that were highly informative, consistently easy to score, provided good genome coverage and could be conveniently amplified into two multiplexed reactions. As a proof of concept, the fingerprinting set was used to genotype 37 red raspberry cultivars of various origins and 19 advanced selections from our breeding programme. The multiplexed set amplified consistently the same products originated by single reactions and it reliably discriminated all non-clonal accessions including full-sib genotypes. Furthermore the set was tested on 19 accessions of eight related Rubus species to assess its transferability. Provided control samples are included, this set will permit research groups to share data accurately and easily. The use of DNA fingerprinting to ensure trueness-to-type of clonally propagated horticultural crops is increasingly common and this multiplexed set constitutes a reliable, convenient and economic tool for raspberry genotyping.