Nagisa Furukawa wrote:
I don't know if we can look too closely to the Targ interbreeding for an explanation of anything. IIRC, Martin has admitted that genetics aren't his strongpoint. In this continuity, all Baratheons have black hair and all Targs have purple eyes and silvery hair; it's not really like real-world genetics apply.
May seem a pedantic point but not ALL Targs have purple eyes and silver hair. Princess Rhaenys took after her Dornish mother not Rhaegar in appearance and Baelor Breakspear in The Hedge Knight also doesn't look traditionally Targ (or traditionally Valyrian). A minor point but an important one given how many times I've heard "But how can Jon be a Targaryen if he's got brown hair?"
There's that, and there also appears to be a clue in the whole Baratheon/Lannister "The Seed is Strong" aspect, where any time a dark-haired individual is introduced into the mix, the blond gene seems to go dormant and the offspring always has dark hair. That was what both John Arryn and Ned Stark had discovered while researching the family lines.
So, if Jon is, in fact, the offspring of Rhaegar Targaryen and Lyanna Stark (who was said to have had dark hair and resembled Arya) as many people think, Jon's dark hair is easily explained through that lineage.
It makes me feel very sorry for Cat, always having to live with the false belief that Jon was Ned's bastard son, that tore her up inside for years. Ned should have told her - straight up. She would have taken the secret to her grave.