Molecular markers and maps are the basis for trait analysis studies and marker-assisted selection. The main objectives of project R6951 were to further saturate the available genetic maps and to produce new, user-friendly markers that could be used to screen breeding materials fast and efficiently. The density of the markers was increased using AFLPs and PCR-based microsatellite markers were generated. These markers were provided to ICRISAT and used for marker-assisted selection to enhance downy mildew resistance in pearl millet hybrids. In addition, a pilot study was carried out to assess the prevalence and use of single nucleotide polymorphism (SNP) as a new marker system for pearl millet. The fact that the first improved variety produced by marker-assisted selection is ready for release to the farmers indicates the success of the pearl millet molecular marker work. The conservation of colinearity between the genomes of different cereal species can be used to enhance the knowledge on all crops. In order for pear millet to benefit from the comparative knowledge, the relationship between its genome and that of rice was established. This will allow the transfer of information and resources from rice and other grass species to pearl millet, for example to tag regions of the genome controlling drought tolerance.