Development and application of functional markers in maize

Functional markers (FMs) are derived from polymorphic sites within genes causally involved in phenotypic trait variation (Andersen, J.R. & T. Lübberstedt, 2003. Trends Plant Sci 8: 554–560). FM development requires allele sequences of functionally characterized genes from which polymorphic, functional motifs affecting plant phenotype can be identified. In maize and other species with low levels of linkage disequilibrium, association studies have the potential to identify sequence motifs, such as a few nucleotides or insertions/deletions, affecting trait expression. In one of the pioneering studies, nine sequence motifs in the dwarf8 gene of maize were shown to be associated with variation for flowering time (Thornsberry, J.M., M.M. Goodman, J. Doebley, S. Kresovich, D. Nielsen & E.S. Buckler, 2001. Nat Genet 28: 286–289). Proof of sequence motif function can be obtained by comparing isogenic genotypes differing in single sequence motifs. At current, the most appropriate approach for this purpose in crops is targeting induced local lesions in genomes (TILLING) (McCallum, C.M., L. Comai, E.A. Greene & S. Henikoff, 2000. Nat Biotechnol 18: 455–457). In central Europe, maize is mainly grown as forage crop, with forage quality as major trait, which can be determined as proportion of digestible neutral detergent fiber (DNDF). Brown midrib gene knock out mutations have been shown to be beneficial for forage quality but disadvantageous for overall agronomic performance. Two brown midrib genes (bm1 and bm3) have been shown to be involved in monolignol biosynthesis. These two and additional lignin biosynthesis genes have been isolated based on sequence homology. Additional candidate genes putatively affecting forage quality have been identified by expression profiling using, e.g., isogenic bm lines. Furthermore, we identified an association between a polymorphism at the COMT locus and DNDF in a collection of European elite inbred lines.