Unique mitochondrial DNA interacting with standard male biology
So, you need an ability which is inherited solely from the mother, but becomes active only in males.
This suggests that you are looking for an interaction between:
- Strictly maternal genes (inherited only from mother - regardless of the father's genes)
- Strictly masculine (male) biology (triggers only in males).
In addition to the DNA in the cell's nucleus (half of which is donated by the father and the other half by the mother), a baby inherits mitochondrial DNA:
Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use[...]. Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus[...].
[...] In most species, including humans, mtDNA is inherited solely from the mother.
The reason mtDNA is inherited solely from the mother is that while the father donates only DNA (32 chromosomes - half of the total in humans), the mother donates an entire living cell (an egg) - which has both a special nucleus with only 32 chromosomes (the matching half of the father's donation - combined they provide a complete set of 64 chromosomes) and all the functioning organelles of a cell, including mitochondria - which happens to have genes of its own.
This can be something like special interaction between the mutated mDNA with typical genes in the Y chromosome (exists only in males), or something much more complex such as different hormonal levels (e.g. high testosterone, low estrogen etc.) - as many of these hormonal differences become pronounced during puberty, the second option may fit better to your narrative.
Combining the two
If your witches have unusual ("mutated") mitochondria, their children will always have them too. Their daughters will be witches and their children will also have these mutated mitochondria, and so will their daughters' daughters etc.
Witches' sons will also have these mutated mitochondria in every cell of their body - but will not pass them to their children. When the mitochondrial "kekai genkai" genes interact with the male biology (either with standard Y chromosome genes or with the different hormonal balances), they will manifest the unique abilities.