Development of simple sequence repeat markers in rye (Secale cereale L.)

Simple sequence repeats (SSRs), also referred to as microsatellites, repres ent a PCR-based marker system that has been described in mammalian and plan t genomes in recent years. In self-pollinating crop plants they have been s hown to be superior to other DNA markers with respect to their level of pol ymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to deter mine the usefulness of SSR markers in rye genetics and breeding, several ge nomic libraries were screened for (CT/GA)(n) and (GT/CA)(n) dinucleotide re peats. It was estimated that these motifs occur at a frequency of one per 2 68-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA )(n) (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulte d in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected het erozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP marke rs in both cultivars.