SummaryRye inbred lines segregating at the S-locus and homozygous at the Z-locus were investigated by PCR with primers derived from Brassica SLG-sequences. After denaturing gradient gel electrophoresis (DGGE), a 280 bp PCR-fregment displays a polymorphism perfectly correlated to the underlying S-genotypes. This is the first report on S-related DNA polymorphism in a bifactorial self-incompatibility system of the Poaceae.made to identify S alleles with molecular methods such as the use of S-specific oligonucleotide probes (Scutt and Croy, 1992) or PCR primers which amplify S allele-specific sequences (Brace et aL, 1993). We report on an alternative approach for S allele identification in rye by denaturing gradient gel electrophoresis (DGGE) of PCR amplification products. The DGGE technique, often combined with PCR, provides a fast and non-radioactive method of analysing DNA fragments of similar size for allelic sequence variation and has successfully been used in plants (Dweikat et aL, 1990; Riedel et aL, 1993). The power of this method is based on altered melting properties of short double-stranded DNA fragments, even in the presence of only single base pair differences.