The candidate gene approach in plant genetics: a review

The candidate gene (CG) approach has been applied in plant genetics in the past decade for the characterisation and cloning of Mendelian and quantitat ive trait loci (QTLs). It constitutes a complementary strategy to map-based cloning and insertional mutagenesis. The goal of this paper is to present an overview of CG analyses in plant genetics. CG analysis is based on the h ypothesis that known-function genes (the candidate genes) could correspond to loci controlling traits of interest. CGs refer either to cloned genes pr esumed to affect a given trait (`functional CGs') or to genes suggested by their close proximity on linkage maps to loci controlling the trait (`posit ional CGs'). In plant genetics, the most common way to identify a CG is to look for map co-segregation between CGs and loci affecting the trait. Stati stical association analyses between molecular polymorphisms of the CG and v ariation in the trait of interest have also been carried out in a few studi es. The final validation of a CG will be provided through physiological ana lyses, genetic transformation and/or sexual complementation. Theoretical an d practical applications of validated CGs in plant genetics and breeding ar e discussed.