DNA polymorphisms are the markers of choice for the identification and characterization of plants. They are an integral part of the plant and they are not subject to environmental modification. There are relatively reliable generally applicable methods to obtain large samples of markers from any species of plant. However, each marker system samples a different fraction of the genome and therefore has a different resolving power, range of applicability and probability of homology. Standard measures (e.g., genetic distance) are dependent on the marker system and on the group under study. Taxa of similar rank may differ greatly in the variability of molecular marker systems. This is illustrated with examples from the genus Allium.At the IPK, a unique living collection of about 300 species of the genus, many collected at type localities, and a large collection of accessions of the cultivated species has been studied with a range of molecular markers: isozymes, RAPDs, ITS-sequences, PCR-RFLPs of variable regions of chloroplast DNA, and genome in situ hybridization (GISH). Molecular marker studies have necessitated changes in the subgeneric classification of the genus but have confirmed the monophyly of most sections within subgenera. The origin of various cultivated groups has been elucidated, especially where material of native origin was available, since garden-grown Alliumare very liable to genetic introgression. Introgression in nature between species from various sections has been demonstrated. Microsatellite primers have been developed for the characterization of individual accessions of Allium cepaand for molecular genetic mapping experiments.

Key words: Allium, chloroplast DNA, hybridization, ITS, phylogeny, RAPD