CMA/DAPI Banding of Plant Chromosomes

Chromosome banding based on base-specific fluorochromes, mainly double staining with chromomycin A₃ (CMA) and 4'-6-diamidino-2-phenylindole (DAPI), has been widely used since the 1970s. This technique allows the differential staining of distinct types of heterochromatin. Afterward, the fluorochromes can be easily removed and leave the preparation ready for sequential procedures such as FISH or immunodetection. Interpretations of similar bands obtained with different techniques, however, merit certain caution. Here we present a detailed protocol for CMA/DAPI staining optimized for plant cytogenetics and call attention to the most common sources of misinterpretation of DAPI bands.