My suspicion has generally been that it has to do with humidity. That is the biggest difference in running conditions between East/Midwest and West. Horses in general prefer lower humidity conditions; the only population of true wild horses was found near the Gobi Desert, after all. The escaped wild horse population in North America stayed pretty much in the low humidity high plains and intermountain regions - they didn't spread to the humid river valleys of the south and Midwest, although they had plenty of time to do so. Human intervention, by taking horses to more humid places (like the British Isles!), has selected for those horses that can tolerate more humidity in the air they breath, but the species preference still unlies these manipulated genes and can come to the fore.
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