Functional markers were defined in 2003 by Andersen and Lubberstedt as “markers derived from polymorphic sites within genes causally involved in phenotypic trait variation”. The starting point for development of a FM is to sequence a gene with known function to obtain polymorphic sequences. Several steps of bioinformatics/statistical analysis are needed; matching of sequence reads to a reference gene, variant detection and association of polymorphic alleles with phenotypic variation.