Molecular Cytogenetic Approaches in Exploration of Important Chromosomal Landmarks in Plants

Multicolored fluorescence-based chromosome biology or ‘molecular cytogenetics’ in common continue to flourish and make essential contributions to elucidate the plant gene regulation, genome architecture, and organization by revealing essential chromosomal landmarks. Fluorescence in situ hybridization (FISH) and its modifications, such as extended DNA fiber-FISH, bacterial artificial chromosome (BAC)-FISH, multicolor-FISH (McFISH), and super-stretched pachytene-FISH, allow the study of minute details of chromosome structure and subsequently permit sophisticated analyses of chromosomal behavior. Similarly, genomic in situ hybridization (GISH) facilitates genome-specific chromosome painting in hybrids and polyploids, analysis of recombination of partially homologous chromosomes in interspecific/generic natural hybrids, and detection of transgene and/or alien chromatin in synthetic hybrids. The global patterns of chromatin modification (e.g., DNA methylation and histone tail modifications) along with nuclear size and shape, relative content and distribution of hetero/euchromatin, and organization as well as structure of chromosomes (e.g., position and orientation) provide new insights into epigenomic evolution of the particular plant species. Molecular cytogenetics also provide information on gene pool diversity and relatedness of the plant to its wild relative that ultimately may serve as a baseline data for plant breeding programs. As more genomes become sequenced, such cytogenetic tools will play a greater role in investigating the function of those genomes. Attempts have been made to summarize the utility of molecular cytogenetic tools in exploration of important chromosomal landmarks in plants. The evolution of plant cytogenetic research from classical to molecular level and modern to next-generation era has been discussed.