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Drosophila polytene chromosomes have been particularly useful in genetic research, as it made cytogenetic gene mapping possible with very little effort. This was primarily accomplished due to polytene bands, which are naturally-occuring (no stain) fixed bands seen along the chromosomes via microscopy.

We have been exploiting these bands for decades, but it seems as though their function isn't quite clear.

What is the cause of the visible polytene bands, and what function do they serve?

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well, Wikipedia says that they are formed by numerous rounds of replication without cell division, and their function may be in gene dosage [but this is not really clear]. However, this is all without proper references, so you should probably wait until someone comes along with citations to verify. –  dd3 Apr 18 '13 at 3:07
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This review has more information than you will ever want to know. –  terdon Apr 20 '13 at 13:53

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