I am not an instructor but let me try to explain why I think B is the correct answer instead of E. (I initially picked E as well).
The main conclusion of the stimulus is "Therefore, pedigree organizations should set standards requiring working ability in pedigreed dogs classified as working dogs".
The word "since" is a premise indictor.
*Since* dog breeders try to maintain only those traits specified by pedigree organizations, and traits that breeders do not try to maintain risk being lost, certain traits like herding ability risk being lost among pedigreed dogs
The word "since" introduces the premise and the conclusion of the above sentence is "certain traits like herding ability risk being lost among pedigreed dogs".
So, by comparing the above conclusion and the main conclusion, it is clear that the above conclusion at the end of the sentence starting with "since" is the sub. conclusion as it supports the main conclusion. It is a sub. conclusion instead of a premise (as what answer choice (E) states) because it has a premise supporting it.