Los marcadores funcionales (FM) derivan de sitios polimórficos del genoma con genes involucrados en la variación de caracteres fenotípicos, y por lo tanto ofrecen ventajas comparativas respecto de otros marcadores «anónimos». El desarrollo de FM requiere de genes caracterizados funcionalmente, secuencias de alelos de tales genes, identificación del motivo polimórfico funcional afectando el fenotipo de la planta, validación de las asociaciones entre el DNA polimórfico y la variación del carácter. Los FM pueden clasificarse como indirectos (IFM) o directos (DFM). En el presente estudio se revisa el estado de investigación desarrolladas sobre el genoma de maíz con respecto al desarrollo de FM, y se ilustra el proceso mediante el desarrollo de FM para calidad de forraje relacionados con un bajo contenido de lignina. LECTURA RECOMENDADA

Thomas Lübberstedt, Imad Zein, Jeppe Reitan Andersen, Gerhard Wenzel, Birte Krützfeldt, Joachim Eder, Milena Ouzunova & Shi Chun 
Euphytica (2005) 146: 101-108

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.