In Situ Hybridization-ISH for Location of Sequences of Chromosomes - A molecular probe can also be used for in situ hybridization where chromosomes in miotic or meiotic preparation are used for hybridization with the probe (without extracting DNA). In a number of cases, rye chromosomes in wheat background have been indentified using this technique.

Sat- chromosomes with NORs (nucleolar organizing regions) are recognized using probes for ribosomal DNA as done in many cases (wheat, barley, etc). Telomeres have been identified in human and other eukaryotes using a telomeric sequence as a molecular probe, showing that telomeres of all chromosomes carry the same sequence.

In wheat and related species, chromosomes of D genome can be identified using a D genome specific probe (pASl separated from Aegilops squarrosa). A large number of such cases can be cited where the use of molecular probes for in situ hybridization served a very useful purpose.