A multiplex SSR system for variety identification of italian bread wheat.

The availability of accurate methods for variety identification is relevant for quality control in the seed sector, as well as for traceability in the food chain production. Due to their high discriminative ability and reproducibility, microsatellites (SSR) are commonly used for genotyping in research and breeding. One relevant aspect for their wide adoption in routine testing is the availability of highly informative multiplex sets, which would allow the cost-effective processing of numerous samples. The aim of this work was to establish a rapid identification system for Italian bread wheat cultivars based on the use of multiplexed SSR. Candidate markers, pre-selected on the basis of available literature for their polymorphism, molecular weight and genomic distribution, were tested for suitability to be combined in multiplex analyses. A set of seven highly informative SSR loci, containing di- and tri-nucleotide repeats and mapping on different chromosomes, was finally identified that could be co-amplified and easily scored after electrophoresis. The discriminatory power of the set was assessed on a panel of 51 bread wheat genotypes including the most prominent varieties currently grown in Italy as well as some old cultivars and recently-developed experimental lines. The multiplexed markers allowed the complete discrimination of all entries: of the 1275 possible pairwise comparisons, just 8 were distinguishable based on one marker only, and for just one of them alleles differed for only 2 nucleotides. The system seems to be a valuable tool for efficient variety identification in bread wheat.