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For a long time,
Arabidopsis thaliana
was not a favorite of cytogeneticists because of its small chromosomes. Nevertheless, most cytogenetic approaches have become applicable to this model plant during the past decade. Recently, the very small genome, the low content, and strong clustering of repetitive sequences even turned out to be advantageous for the first establishment of chromosome painting in a euploid plant. Chromosome painting together with the high-resolution fluorescence
in situ
hybridization (FISH) mapping on
Arabidopsis
pachytene chromosomes has opened new perspectives for plant cytogenetics.In this chapter, we describe standard cytogenetic methods including preparation of chromosomes and chromatin fibers, isolation of interphase nuclei, FISH and immunostaining, painting of
Arabidopsis
chromosomes, and comparative chromosome painting in other
Brassicaceae
species.