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I agree with nchen7, you should check up on the info on the link about Johnes.
As for registration, whether you go with AGA or ADGA should I guess depend on what you plan on breeding or doing. I just got goats from someone that was originally in AGA but switched to AGS. I don't really know too much about AGS or AGA so I will be dual registering them with ADGA. I really like ADGA because they have some great options like being able to register online, search pedigrees, and in my area they are affiliated with all our dairy shows. I would say if your doing a lot with dairy breeding and want to show consider going with ADGA because they're the biggest and most popular but you can always have you goats dual registered. ADGA should accept registration and papers from another group as proof of the goats breeding. If you aren't interest in showing then AGS or AGA could probably work. I would do a lot of research on either though, just to make sure it's a good fit for you.
As for registration, whether you go with AGA or ADGA should I guess depend on what you plan on breeding or doing. I just got goats from someone that was originally in AGA but switched to AGS. I don't really know too much about AGS or AGA so I will be dual registering them with ADGA. I really like ADGA because they have some great options like being able to register online, search pedigrees, and in my area they are affiliated with all our dairy shows. I would say if your doing a lot with dairy breeding and want to show consider going with ADGA because they're the biggest and most popular but you can always have you goats dual registered. ADGA should accept registration and papers from another group as proof of the goats breeding. If you aren't interest in showing then AGS or AGA could probably work. I would do a lot of research on either though, just to make sure it's a good fit for you.