I'm not necessarily sure its the breeding, but the upbringing. A dog that is taken from its mom and other pups at 7-8 weeks old and is then well cared for and begins training is just so much more likely to be an obedient and well behaved pet.
In a book I read about training hunting dogs (water dog), the author mentions he participated in a study where pure bred labs were trained for service dog work (for the blind). Intensive training starts at 1 year of age. Labs that were taken at the age of 7-8 weeks and then put into a household where the owner taught them basic obedience (crate training, sit, stay, fetch, lay down) made it through the program 90% of the time.
The dogs that started the intensive training at 1 yr that did not have this background (some would get taken from the mom at older or younger ages, and hardly receive any obedience training) only made it through the class 60% of the time.
The age at which they are taken into a household is a big factor.
That's the nature vs. nurture debate, and I think it's both. Everyone, dogs included, inherit traits from their parents. I look at the parent dogs, at their behavior. It can't all be trained. I want stable, calm, well socialized parents, not skittish or snappy dogs. Also good structure. I wont get into it, but there is an entire system of dog testing and qualifications required for breeding German Shepherds in Germany, where all my dogs originated. In the US, anyone can breed anything and get papers that mean virtually nothing.