One thing too was that during the Nez Perce wars and after, to ruin the breed the Army turned all sorts of scrub stallions in, killing off the prized Appaloosa stallions of the tribe.
When the herds were first seen, it was said they numbered in the thousands...and many of those were Appaloosas. The Nez Perce were fine horsemen, Lewis and Clark recognized that, and remarked that their castration technique was superior to their own.
One reason for the attempted destruction of the breed, was to make sure the Nez Perce would be without their horses, many of the horses surrendered after Chief Joseph and his band tried to flee the US, were either shot immediately, or were shipped back East. Horses that still roamed the land, were hunted down too.
Some horses were rounded up by whites and quietly bred also. These horsemen were the saving of the breed in many ways. Had they not done that, there is no telling what would have happened.
Just a wonderful breed though, darn shame so much has been done to them in centuries past.
For those that like to read, here are some interesting links. Appaloosa Livestock Profile Chief Washakie Foundation History of the APPALOOSA and the NEZ PERCE Appaloosa History Appaloosa Horses & Nez Perce Culture