Your coats, eyes, and nose have different rarities(common, uncommon, rare, legendary, and dynamic(only for coats)). The rarer, the higher the rarity score.
Markings also add to the rarity score. The more markings, the higher the over all rarity score
I recommend breeding for both, rare coats, eyes, amd noses and many markings. The cheaper way is probably just to search by rarity in the trading post and finding a cheap, high rarity stud for your females. Breed to him, get the pups and keep trying to get pups with higher and higher scores.