Isolation and chromosomal distribution of a novel Ty1-copia-like sequence from Secale, which enables identification of wheat-Secale africanum introgression lines

A repetitive sequence of 411 bp, named pSaO5₄₁₁, was identified in the Secale africanum genome (Rᵃ) by random amplified polymorphic DNA (RAPD) analysis of wheat and wheat-S. africanum amphiploids. GenBank BLAST search revealed that the sequence of pSaO5₄₁₁ was highly homologous to a part of a Ty1 -copia retrotransposon. Fluorescence in situ hybridization (FISH) analyses indicated that pSaO5₄₁₁ was significantly hybridized to S. africanum chromosomes of a wheat-S. africanum amphiploid, and it was dispersed along the Secale chromosome arms except the terminal regions. Basing on the sequence of pSaO5₄₁₁, a pair of sequence-characterized amplified region (SCAR) primers were designed, and the resultant SCAR marker was able to target both cultivated rye and the wild Secale species, which also enabled to identify effectively the S. africanum chromatin introduced into the wheat genome.