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Equestrian Genetics of My Little Pony
Equestrian Ponies have from what I can gather a Trinary Paired genetic system.
genetically, there are three Genetic divisions, Unicorn, Pegasus, Earth Pony.
now while a dominant trait will win over a non-dominant one
with a trinary pair it can also act kind of like a vote, with a non dominant acting as a tie breaker between two dominant genes.
An Alicorn ascended and natural, carries three Dominant genes of each tribe,
a Unicorn must have at least one dominant Unicorn gene. The most powerful thoroughbred Unicorns such as starswirl, Twilight, and shining armour each originally had 3 dominant Unicorn genes.
Applejack probably has 3 Dominant Earth genes, and Rainbow probably has 3 Dominant Pegasus genes
average ponies usually only have one dominant gene, the other two being non-dominant, or 2-3 matched non-dominant genes
Pinkie Pie while appearing as a normal earth pony, displays abnormal magical feats,
given her family history pinkie obviously has two earth Genes, one or both being dominant,
her third Gene could however be a dominant unicorn gene.
the same could be said with Fluttershy’s affinity towards nature and animals
Two Pegasus genes, one or both being dominant, and a dominant Earth gene
Rarity is a higher than average Unicorn, probably having 2 Dominant Unicorn genes,
and the third being a non-dominant unicorn gene.
as for Flurry, it’s obvious shining Armour as the father supplied a dominant Unicorn Gene
and Cadance as an Alicorn and the mother, provided both a dominant Pegasus, and a dominant Earth gene.
the Cake twins, Two Earth pony parents.
carrot cake has 2 Earth Genes, Dominant, and non-dominant, and a dominant Unicorn gene
Cupcake has 2 Earth Genes, Dominant, and non-dominant, and a dominant Pegasus gene
pumpkin inherited the Unicorn gene, and two non-dominant earth genes
Pound inherited the Pegasus gene, and two non-dominant earth genes
meaning that both parents provided 2 thirds of a Trinary Paired set
but that the magic of conception, randomly discarded the extra third.
given that an Alicorn carries three Dominant genes of each tribe
a winged unicorn would have three Non-dominant genes of each tribe
or dominant Pegasus and Unicorn Genes, but a non-dominant earth gene.