ABSTRACT
Candidate gene analysis for defining the molecular genetic basis of simply inherited phenotypic traits typically consists of four steps. First, one or more candidate genes are proposed according to cause-effect relationships that have been previously observed in the investigation of similar phenotypes in model species (such as Arabidopsis thaliana), or alternatively, based on rational predictions deduced from an understanding of metabolite flow through well characterized biochemical pathways. Second, molecular polymorphisms having the potential of altering gene function are identified in the candidate gene between genotypes exhibiting measurable variability at the investigated trait. Third, an association is established between the molecular polymorphism and phenotype in question in a population segregating for the trait. Fourth, the candidate gene is validated. In cases where a mutation in a gene is believed to be responsible for the trait in question as a consequence of gene dysfunction, the ultimate means of verification is to demonstrate functional complementation through transgenic expression of the wild type gene.
