Great advances have been made in recent years in marker detection systems and in the techniques used to identify markers linked to useful traits. While RFLP markers have been the basis for most work in crop plants, useful markers have been generated using RAPD and AFLP methods. More recently, microsatellite or simple sequence repeat (SSR) markers have been developed for major crop plants and this marker system is predicted to lead to even more rapid advances in both marker development and implementation in breeding programs. Identification of markers linked to useful traits has been based on complete linkage maps and bulked segregant analysis. However, alternative methods, such as the construction of partial maps and combination of pedigree and marker information, have also proved useful in identifying marker/trait associations. The value of markers in analysing the inheritance of traits in crop plants and understanding genome structure and organization is now well established. The different properties of markers systems and their applications in genome analysis and molecular breeding of cereals species are discussed.
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