What is the difference between Merle and Harlequin Merle?

The difference between a standard Merle and a Harlequin Merle comes down to the length of the genetic insertion at the Merle gene locus (SILV or PMEL17).

• Standard (or Classic) Merle: Dogs with a normal merle pattern have an insertion length of 78 to 86 base pairs at this locus. This length creates the classic merle coat, which consists of a mosaic pattern of fully pigmented dark areas mixed with diluted background areas.

• Harlequin Merle (M 

h

 ): Dogs with the Harlequin Merle mutation have a longer insertion of 81 to 105 base pairs. This specific length causes the dog to have large areas of pure white coat alongside areas of fully pigmented coat. While the standard Harlequin modifier is only found in Great Danes, this specific Harlequin Merle variation can sometimes be seen in other merle breeds.

Confusion with the Harlequin Modifier (H Locus). It is important not to confuse the Harlequin Merle variation with the true Harlequin modifier.

As discussed previously, the traditional Harlequin pattern found in Great Danes is caused by the interaction of a normal merle gene and a completely separate modifier gene located on the H locus (PSMB7). Most Great Danes that exhibit a harlequin pattern achieve it this way: they inherit a normal merle insertion length combined with one copy of the Harlequin modifier (H), which acts to remove the dilute background pigment.

However, because the Harlequin Merle insertion can independently create a harlequin-like pattern of large white and fully pigmented areas, researchers have discovered that a small number of Great Danes are harlequin due to this mutation

  rather than the PSMB7 modifier. Therefore, genetically speaking, there are two different ways for a Great Dane to have a harlequin appearance.