A representative, highly informative 'genotyping set' of barley SSRs

We have developed a 'genotyping set' of 48 SSR-based genetic markers for ap plication in genetical studies of barley. The SSRs are a subset of a collec tion of approximately 600 SSRs available to the barley research community. They have been specifically chosen according to the following criteria: (1) they are single locus; (2) their product quality is good under standard as say conditions; (3) they are distributed across the barley genome; and (4) they exhibit reasonably high polymorphic information content (PIC) values i n the cultivated barley gene-pool. To maximise genotyping throughput, one o f each SSR primer pair was 5 ' end-labelled with either fam, hex or tet flu orochromes to allow automated data capture after running the samples on a D NA sequencer. SSR product sizes were assembled from a reference set of 24 b arley genotypes which allowed the construction of 'graphical genotypes' of each of the individual lines. The graphical genotypes provide a convenient tool for interrogating genetic similarity in the individuals surveyed. The product sizes were compared to those obtained from end-labelling one of the primers with P-33 and separating the products by denaturing PAGE followed by autoradiography. Although inconsistencies in size were common, they coul d generally be easily resolved. A reference manual for use of the 'genotypi ng set' has been produced and is available as a PDF download file at http:/ /www.scri.sari.ac.uk/ssr/pdf. These well-characterised barley SSRs, for the first time, provide a common set of robust PCR-based tools which can be us ed to integrate and compare information collected from fundamental and/or a pplied genetic studies on barley in different laboratories across the world .