I have a sylesti, he's a hatchling named Digi, https://www.sylestia.com/view/pets/?petid=3992239 He just hatched and I was surprised to find he has Digital Runes. His father, https://www.sylestia.com/view/pets/?petid=707005, has rainbow life runes. And his mother, https://www.sylestia.com/view/pets/?petid=3943892, has nothing.

Where did he get this gene? Both of his parents don't have parents since they were spawned by the game, so, where could he have gotten it?

Genetics work like this:

Un-named Fawn Zolnixi (Digi's father) has carried gene 3 (and mutation one and two, not really needed here in explaining Digi's visible g3). Un-named's g3 is (ND), or carried Rainbow Life Runes because he has nothing (N) in the first spot, and (D) being the carried Runes.

Vanessa is a mystery. She hasn't been genetically tested. There's no way to tell if she's carrying anything without testing her. I'm guessing she has carried Digital Runes in her g3 spot (NB).

If Un-named passed on his (D) and Vanessa passed on her (B) for g3, then Digi actually has (BD) is his g3 spot, but you see (BB) there because he hasn't been genetically tested, but you can infer (BD) because his father has (D). And, of course, the reason Digi shows Digital Runes instead to Rainbow Life Runes is because (B) for Digital Runes comes alphabetically before (D) for Rainbow Life Runes.

Digi could also be possibly carrying his father's m1 or m2, or maybe even Vanessa has more hidden traits that you don't know of.

I hope this helped and explained effectively to you the reason as to why Digi has Digital Runes.