“Principle and Procedures of Genome Analysis”

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

M.Sc. Seminar - GPB 581 (0+1)

“Principle and Procedures of Genome Analysis”

The term ‘‘Genome Analysis’’ circumscribes scientific approaches and methodologies that aim at elucidation of the structure, evolution, and function of whole genomes rather than individual genes. Analysis of plant genomes began with the cytogenetic description and identification of the 10 chromosomes of maize (Zea mays). To date, cytogenetic approaches are still, or again, important tools for the structural analysis of plant genomes.¹

There are many cytogenetic approaches to study the higher order organization of the chromosomes. Chromosome staining allows the proper visualization of chromosomes by using different staining techniques.² Cytogenetics entered the molecular era with the development of the in-situ hybridization technique, in which a labeled nucleic acid probe is hybridized to denatured DNA of chromosomes spread on a microscope slide. Since then, radioactive labeling methods have been replaced by fluorescent in situ hybridization (FISH). FISH also allows the simultaneous use and detection of several probes, each one labeled with a different fluorochrome (Multicolor FISH). Total genomic DNA of a given plant species can also be specifically labeled with a fluorochrome and used as a probe in genomic in situ hybridization (GISH).³

Chromosome staining has been successfully applied to study the karyotypic diversity in untapped cultivars to expand the chromosomal database and untapped gene pool. For example, a study on the karyotype diversity in some valuable and mostly traditional non-aromatic and aromatic Indian rice cultivars through EMA-based Giemsa and DAPI staining found cultivar-specific variations in karyomorphological features and the unique diversity in the number of chromosome pairs featuring secondary constrictions, which affirms ongoing intra- and inter-specific chromosomal rearrangements.⁴

Molecular cytogenetics techniques are most widely used to study the genome composition of some crops. One such study analyzed eight popular Narcissus cultivars using GISH and/or FISH techniques, which clearly revealed their genome composition, ploidy levels along with their origin, and reported the variation of 5S and 45S rDNA sites. Based on the cultivar’s genome composition and origin, it was concluded that distant hybridization, sexual polyploidization, and chromosome doubling play different roles in breeding modern Narcissus cultivars.⁵

Cytogenetic methods are vital for unraveling plant genome complexity, enabling the study of polyploidy, chromosomal rearrangements, and species evolution via techniques like FISH and karyotyping. Their integration with next-generation sequencing enhances crop breeding, biodiversity conservation, and the development of resilient agricultural varieties.

REFERENCES:
1 GEBHARDT, C., SCHMIDT, R. AND SCHNEIDER, K., 2005, Plant genome analysis: the state of the
art. Int. Rev. Cytol., 247:223-284.
2 ESTANDARTE, A.K.C., 2012, A review of the different staining techniques for human metaphase
chromosomes. Department of Chemistry, Univ. Col. Lond, Univ. Lond.
3 SHAKOORI, A.R., 2017, Fluorescence in situ hybridization (FISH) and its applications.Chromosome
structure and aberrations,.343-367.
4 JHA, T.B. AND HALDER, M., 2025, Unlocking karyotype diversity in some valuable non-aromatic and
aromatic indian rice cultivars through EMA-based Giemsa and DAPI staining. Genet. Resour. Crop
Evol.,1-19.
5 SUN, Y., ZENG, J., LIU, S. AND ZHOU, S., 2024, FISH and GISH reveal genome composition of popular Narcissus cultivars and the possible ways of their origin. Euphytica, 220(6),82.

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