Comparative analysis of plant genomes using advanced fluorescent in-situ hybridization (FISH)

During speciation, chromosome segments may change position on chromosomes through translocations and inversions. Such structural rearrangements can be visualized using microscopy and advanced fluorescent in-situ hybridization (FISH). We use this approach to investigate structural rearrangements between different species.

In recent years, many genome sequences became available for (crop-) plants. It is possible to use these genome sequences to design sets of fluorescent probes (oligos) that can be used to visualize specific regions on plant chromosomes. This technique is known as oligo-FISH. Such probe-sets can be used to investigate visualize and identify structural variation between the genomes of related species.


Visualizing structural variation using oligo-FISH may be used for various purposes, of which two have our special interest.

Structural variation between species can be used for reconstruction of phylogenies, when is investigated to what extent species share-, or differ in the presence of structural variants.

Alternatively, the presence of structural variation between species may severely complicate the pairing of chromosomes during meiosis, and may prohibit the introgression of traits from wild species into crops. Using oligo-FISH one can study in detail how specific chromosome segments behave during introgression breeding.


For experiments, plant material has to be collected from which chromosome spreads (slides) are made that can be used in FISH experiments. These slides may be made from root tips (mitotic cells) or from flowerbuds (meiotic cells).

Pools of oligos are designed, and thereafter hybridized to the chromosome spreads after which the hybridization pattern is studied using a fluorescent microscope.

Research projects may involve crops or wild species, depending on the precise research question at hand.

Student Opportunities

We are open to applications for thesis projects! We have different thesis topics available, including projects with Microscopy, Lab work and Slide Preparation.

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