First results on SNP-scanning in fragments linked to resistance genes against the barley yellow mosaic virus complex

Concerning barley yellow mosaic virus disease (BaMMV, BaYMV, BaYMV-2), different recessive resistance genes have been mapped in the barley genome and closely linked PCR-based markers have been developed, e. g., for rym4, rym5, rym9 and rym11. However, these markers are often specific for the populations they have been developed in and, therefore, cannot be widely applied in practical barley breeding. In order to develop a set of markers enabling efficient marker-based selection procedures for these genes in each cross combination (diagnostic markers) as well as for the screening of large germplasm collections with respect to these genes, known sequence-tagged sites (STS) linked to these genes as well as newly developed ones, like STS-OPG06H532, are analyzed for single nucleotide polymorphisms (SNPs) mainly using the fluorescence-detected BESS-T-SequencingTM on an automated DNA-sequencer. Using this approach, three STSs linked to rym4/rym5 and rym11, respectively, have been analyzed on genotypes comprising exotic resistant germplasms, high yielding cultivars and resistant exotic Hordeum vulgare ssp. spontaneum genotypes. Within this set the variation of SNPfrequency in the respective STSs was preliminary estimated at 1(SNP)/116bp to 1(SNP)/266bp. It turned out the respective SNPs are combined to different haplotypes facilitating the efficient development of a set of diagnostic markers based on this sequence variation.