Molecular markers offer numerous advantages over conventional phenotype based alternatives as they are stable and
detectable in all tissues regardless of growth, differentiation, development, or defense status of the cell are not confounded
by the environment, pleiotropic and epistatic effects. Functional markers (FMs) are a good “translator” of gains from
emerging technologies into improved crop cultivars. FMs are derived from polymorphic sites within genes causally
involved in phenotypic trait variation. Once genetic effects have been assigned to functional sequence motifs, FMs
derived from such motifs are used for fixation of gene alleles in a number of genetic backgrounds without additional
calibration. FM development requires (1) functionally characterised genes, (2) allele sequences from such genes, (3)
identification of polymorphic, functional motifs affecting plant phenotype within these genes and (4) validation of
associations between DNA polymorphisms and trait variation.