Development of SCARs by direct sequencing of RAPD products: a practical tool for the introgression and marker-assisted selection of wheat

RAPD markers generated by mixtures of two different primers were developed for octoploid × Tritordeum (amphiploid Hordeum chilense × Triticum aestivum) and its parents. Addition lines were used to identify 21 specific RAPD markers for the H. chilense chromosomes detectable in a wheat background. Ten RAPD bands were selected and eight of them were converted into dominant SCAR markers by direct sequencing of the RAPD products, avoiding the costly and time-consuming cloning step. The methodology overcomes some of the pitfalls associated with the election of the right clones when developing SCARs from RAPD markers. The SCARs generated have maintained both the chromosome specificity and the possibility of detection in a wheat background. This strategy provides a rapid method for the characterization of RAPD markers and for the development of PCR-based markers for both the characterization of the introgression of H. chilense in bread and durum wheat, as well as the efficient and reliable screening of tritordeum lines.