Development and Application of Functional Markers

The value of anonymous genetic markers such as random DNA markers (SSRs, AFLPs, RFLPs etc.) depends for various applications on the known linkage phase between marker and target locus alleles (Lübberstedt et al. 1998). Thus, (quantitative) trait locus mapping is necessary for each cross de novo, as different subsets of QTL are polymorphic in individual populations, and linkage phases between marker and QTL alleles can disagree even in closely related genotypes. In contrast, “functional markers” (FMs) (Andersen and Lübberstedt 2003) are a good “translator” from genomic technologies into improved crop varieties. FMs are derived from polymorphic sites within genes, quantitative trait nucleotides (QTN) or quantitative trait insertion – deletion mutations (QTINDEL), causally affecting phenotypic trait variation. Once genetic effects have been assigned to functional sequence motifs, FMs can be used for fixation of beneficial alleles. FM development requires (1) functionally characterized genes, (2) allele sequences from such genes, (3) identification of polymorphic, functional motifs affecting plant phenotype within these genes, (4) validation of associations between DNA polymorphisms and trait variation, and (5) conversion into technical assays using, e.g., any of the single nucleotide polymorphism (SNP) or INDEL detection technologies (Syvänen 2001).