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Well its part of the breed standard and a lot of the culls were written to make the Boer the hardiest breed possible. Blue eyes don't contain as much pigment as brown ones. This makes it rougher for them in sunnier climates , like those that the Boer originated from.
 

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Only breed that has blue-eyes in the standard is Nigerian Dwarfs. Any other goat that has blue-eyes was crossed somewhere in their lines with a Nigerian. Mini breeds like Mini-Nubian, Mini-Oberhasli, Mini-Manchas can have blue-eyes too though there is some debate in mini breeders whether they should be allowed to be blue-eyed. I personally think its ok.
 
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