The structural characteristics of chromosomes can be seen in chromosomal bands and karyotypes, which is the definition of cytological markers. The color, width, sequence, and placement of the banding patterns show how euchromatin and heterochromatin are distributed differently. For instance, Giemsa stain produces G bands, Quinacrine hydrochloride produces Q bands, and R bands theopposite G bands. These chromosome landmarks are frequently used in physical mapping and linkage group identification in addition to being used to characterize normal chromosomes and detect chromosome mutation. The physical maps based on morphological and cytological markers provide a solid platform for the foundation of genetic linkage mapping.However, there are many restrictions on how directly cytological markers can be applied to genetic mapping and plant breeding. A practical framework for studying a single chromosome, a chromosomal area, or the genomes is provided by the FISH and GISH techniques for examining a single chromosome, a chromosomal region, or the genomes of naturally occurring and artificially created by hybrid plants

Keywords : somoclonal variation, phylogenetic relationship, cytological markers, karyotyping, GISH, FISH, Insitu hybridization, chromosome banding, genome analysis, chromosome mapping, alien chromatin detection portryal in Plants.