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A kekai genkai is a bloodline ability that is passed down genetically within clans. They give users access to specific powers unique to that family. These abilities take a number of forms: going bones out of one's body to make weapons, psychic abilities, super strength, seeing the mana flow of others, etc. Bloodline abilities are very rare, and the clans who have access to them are often very powerful or very feared in their society.

Witchcraft is practiced exclusively by women, and is a complex and drawn out process. Most receive some level of training in it. Bloodline abilities are passed down the female line, as women are the genetic carriers for them. However, they only manifest in males. They first activate around puberty, and becomes more developed with age and training. They cannot be taught or copied by others, so remain exclusive to males specific from that clan. How could it be possible that a genetic ability would activate only in males when females are the carriers of it?

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  • $\begingroup$ There are quite a number of conditions passed down the female line and which manifest only (or, at least, mostly) in men. Why doesn't the ordinary X-linked recessive inheritance pattern work, as in, e.g., haemophilia and color blindness? $\endgroup$
    – AlexP
    Commented Dec 27, 2018 at 11:41
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    $\begingroup$ @AlexP X-linked traits are not only transmitted down the female line. An XX woman passes one of her X chromosomes to her XY son, who will then pass it on to any XX daughters, and so on. The only reason we don't see this happening much with Hemophilia A & B is that historically, males with the defective alleles didn't usually live long enough to father children. $\endgroup$
    – G_B
    Commented Dec 27, 2018 at 12:46
  • $\begingroup$ @GeoffreyBrent: Does the question say "exclusively" down the female line? I'm not seeing it. $\endgroup$
    – AlexP
    Commented Dec 27, 2018 at 15:28
  • $\begingroup$ @AlexP it doesn't explicitly say "exclusively", but it's strongly implied by context and Grice's maxims. If the intention is to have it transmitted by fathers as well, why would the OP bother to specify "passed down the female line"? $\endgroup$
    – G_B
    Commented Dec 27, 2018 at 22:05

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Besides "its on the X chromosome" you could use another type of mitochondria. Mitochondria are important for cells to generate energy, and mitochondria literally have seperate DNA from humans as they are a symbiote that is basically absorbed into humans. Sperm does not contain mitochondria so its only inherrited from the mother (means men only have the mothers mitochondria as well).

They could have rare versions that have powers activated by hormones, making sex-specific magic and abilities possible.

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    $\begingroup$ This is actually a better answer than an X-linked trait, because men can pass on X-linked traits to their daughters. $\endgroup$
    – G_B
    Commented Dec 27, 2018 at 13:10
  • $\begingroup$ That is possible, too, but both males and female embryos have mitochondrias. They are passed-on only by the mother. $\endgroup$
    – Christmas Snow
    Commented Dec 27, 2018 at 14:08
  • $\begingroup$ @Christmassnow yes that is what "it's only inherited from the mother" means. $\endgroup$
    – Demigan
    Commented Dec 27, 2018 at 15:15
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    $\begingroup$ I like this for matrilineal, better than the X chromosome. Since all magic systems are means to manipulate energy, it makes sense that the energy producing components of the cell would be involved. To prevent expression of the magic allele, have it triggered by levels of testosterone. $\endgroup$
    – pojo-guy
    Commented Dec 27, 2018 at 19:50
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    $\begingroup$ @ChristmasSnow this is true, but it's easy enough to handwave an interaction that means the effects are only visible in XYs. $\endgroup$
    – G_B
    Commented Dec 27, 2018 at 22:08
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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:

  1. Strictly maternal genes (inherited only from mother - regardless of the father's genes)
  2. Strictly masculine (male) biology (triggers only in males).

Maternal genes

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. (from Wikipedia)

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.

Male biology

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.

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Since your question reminds me of "Naruto" I would say that going into a fictitious way would be better for you than sticking with a real fact like chromosomes, testosterone or that stuff.

Maybe you can invent some kind of mana or chackram flow that is exclusive for males. Like primal Izanagi chakram (Male Japanese father God). The woman's then would have (Izanami's Chackram).

So maybe males can awaken this ability by stimulating the genetic information that the woman passes her son with her natural chakra.

As a resume: Women give the weapon (Genetic physical sturdiness or characteristic) and the male generates the bullets with his natural chakram (Has the power to awaken the mechanism and use it).

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    $\begingroup$ +1 Good common sense here. The idea of gender-only abilites has been exploded in many fantasy settings, and nearly no one bothered with genetics or any kind of explanation whatsoever. It's just the premise. $\endgroup$
    – Rekesoft
    Commented Dec 27, 2018 at 12:47
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Passed by the females means it's on the X chromosome.

Showing up at male puberty says that it's triggered by testosterone. Since women don't experience male-level testosterone the abilities never show up.

Since as Geoffrey points out this permits transmission from those who actually manifest the power we need one more step--when the power manifests it produces a protein that breaks the gene responsible so it can't be inherited.

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    $\begingroup$ Males can also pass X chromosomes to their daughters, so this wouldn't achieve female-line-only transmission. $\endgroup$
    – G_B
    Commented Dec 27, 2018 at 12:40
  • $\begingroup$ @GeoffreyBrent Ouch, you're right. Adding to my answer... $\endgroup$
    – Loren Pechtel
    Commented Dec 28, 2018 at 0:49
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If you're speaking of humans, there are two ways to do it:

First method the gene manifestation is hormone-dependent. This is the simplest, but may be manipulated with hormone therapy.

Second method: Direct manipulation of the sex chromosomes. Females have two identical chromosomes, XX and men have two different ones, XY. All other chromosomes are not gender-related and are equally present in men and women. You may use the two scenarios:

  1. A trait unique to males: It is on the Y chromosome. The gene has to be active even as a single allele, that means, even though the Y does not have another Y pair, but an X with a different set of genes. The gene is located on the part of the Y which does not recombine.

  2. A trait unique to females: Located on the X chromosome, so both males and females have it. The gene should be active only when it's paired with another X bearing the same gene so that it manifests itself in women only.

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    $\begingroup$ Note that you can't have a strictly maternal bloodline based on sex chromosomes - a father will pass his X chromosome to his daughters... $\endgroup$
    – G0BLiN
    Commented Dec 27, 2018 at 13:35
  • $\begingroup$ In case you need that the gene be active only among females, it must be active when the embryo receives a pair of X (one from mother, one from father), i.e. the embryo is a female. If the embryo is XY (male), he has one X from the mother and Y from father. The X-gene is "lonely" and therefore inactive. Some of the X genes are just like that, so the male does not have developed female organs. $\endgroup$
    – Christmas Snow
    Commented Dec 27, 2018 at 14:10
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X chromosome recessive, like hemophilia. However, having two copies of the recessive gene is lethal, much like sickle cell anemia only more so.

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    $\begingroup$ Genetics doesn't work that way--recessives on the X chromosome manifest when a male gets a single copy of them. That's why hemophilia is far more common in men than women. Thus your men get death, not abilities. $\endgroup$
    – Loren Pechtel
    Commented Dec 27, 2018 at 5:21
  • $\begingroup$ A better but still incomplete solution is a two genes, with one being a recessive on the x chromosome, and the other being a recessive on another chromosome. $\endgroup$
    – pojo-guy
    Commented Dec 27, 2018 at 11:57
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Initiation

Puberty is celebrated in various societies around the world - the debutants. This old tradition is all about "showing off this new member of society", and this could be a point for you to explore. If abilites are rare and treasured, it should be natural that people would want to celebrate it. You could make it so that this "ritual" is also what triggers the activation of such powers.

The Power of BS

Your world has magic, so you can just BS your way out of this situation, since your story seems to be set in a high fantasy kind of world. BS explanations migh include, for example, chromossome Z or S (or any letter. Z already exists, if I'm not mistaken), only present in men.

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Womb Attack

It is somewhat understood that pregnancies of males can cause immune responses in the carrying mother. Could it be that the immune response of a mother to her own child causes the child's latent ability to awaken? This awakening as a fetus could be the impetus to his development of said abilities, since women are the carriers of the ability. Maybe all of her children have the power latent within them, allowing future generations to inherit it, but the internal struggle of mother and child causes it to manifest.

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