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There are many breeds of rare horses. Many of them are rare as they have been developed in mainly isolated areas from select stock and not sold to outsiders or bred elsewhere. After horses have attained a recognizable difference from the foundation stock that can be reproduced it can be considered a new breed (to a degree, there are a couple more rules I'm sure). There are also breeds which are rare as the result of disease, resource limitation, and other limiting factors.
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