Use of molecular markers for the development of new cultivars and the evaluation of genetic diversity

Molecular markers bring new information on the determinism of trait variation and the organisation of genetic diversity within plant species of agricultural interest. We review here how this information can be used to increase the efficiency of plant breeding programs, considering both theoretical analyses and recent experimental data. Use of mapping information to assemble alleles of interest is discussed first, considering an increasing complexity in trait determinism and its consequences on the breeding schemes. Experimental data now confirm the efficiency of these approaches. They call however, for (i) a better modelling of phenotype determinism, to better anticipate the final effect of marker assisted selection and (ii) studies that would address trait variation determinism within a broad diversity, to increase the probability to identify alleles of key interest and identify stable marker-trait associations. Recent promising developments in genetic diversity analysis are discussed with respect to these last objectives.