Identification of microsatellite polymorphisms in an expressed portion of the rye genome

For the purposes of genetics and application the number of simple sequence repeat (SSR) markers in rye has to be increased significantly to cover the entire genome. To this end, more than 8000 publicly accessible rye cDNA sequences from anthers, cold-stressed leaves, and aluminium-stressed and unstressed roots were exploited as a resource for SSR marker development. A total of 157 Secale cereale microsatellite (SCM) loci out of 528 SSRs comprising di-, tri- and tetra-nuelcotide motifs could be assayed on automated sequencers. One-hundred expressed sequence tag (EST)-derived SCM loci displayed a length polymorphism among a sample of 15 rye accessions. Of the SCM, 45% could be associated with proteins of known or unknown function. Recently published ESTs from different rye tissues proved to be a valuable resource Cor SSR marker development in rye.