Low Level of Linkage Disequilibrium at the COMT (Caffeic Acid O-methyl Transferase) Locus in European Maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

During recent decades, the whole plant yield of European maize (Zea mays L.) has increased substantially. However, during the same period of time cell wall digestibility, and consequently fodder quality, has decreased. Alleles for digestible cell walls have thus been lost, either during breeding for stalk standability or by genetic drift during breeding for grain yield. The brown-midrib 3 mutant (bm3) in maize (Z. mays L.), controlled by the caffeic acid O-methyl transferase (COMT) locus, has a positive influence on maize fodder quality. In this study, 42 European maize lines were used to evaluate the nucleotide diversity and linkage disequilibrium (LD) pattern across 2.3 kb of this locus. In agreement with what has been found for other maize loci, we found high diversity values (π = 0.00834), rapid LD decay even in an elite line sample, and indication of selection as well as of recombination events for seven site combinations. The diversity values differed slightly between inbreds of the Flint and Dent pools and most haplotypes were specific for one of the two heterotic groups. The polymorphisms identified at this single locus enable the construction of single nucleotide polymorphisms (SNP) and indel markers for haplotype identification and a rough discrimination of inbreds into Flint and Dent heterotic groups. The results reported here document the degree of allelic diversity in breeding materials and allow for targeted search of novel alleles in genetic resources.