The reason I am not willing to just let mother nature take her course and let two random dogs breed together, is because I am not tough and uncaring like mother nature. If one puppy in 100 in a certain line is born with some eye disease that makes them go blind, mother nature really does not care. Enough puppies with good vision will be born to carry on the line. In my breed Progressive Retinal Atrophy is in our gene pool, and mother nature REALLY does not care about eliminating that one because in our version of the disease symptoms do not appear until the dog is old enough to have reproduced several times.
Mother nature does not care if dogs get crippling hip arthritis when they are older. As long as they survived long enough to reproduce, mother nature is happy.
I, on the other hand, care a whole lot about each and every puppy I produce, and about the families that are investing their love in this puppy. I will make sure that there is absolutely no chance of any puppy I produce having PRA. I will do what I can to avoid producing puppies with hip dysplasia. And many other issues.
The main reason that I tell people that you need to go with a breeder who is dedicated to their breed and has been involved with and learning from other breeders for years is the knowledge that person has. It really has nothing to do with color patterns, length of tail, etc. (Well, I do care when picking out a puppy for a show dog, but beyond that it really does not matter.) Let me give you two examples. And yes it is getting closer to rocket science all the time. ;-)
In my breed, PRA (progressive retinal atrophy) makes dogs gradually go blind. Symptoms may not be noticed until the dog is five, six, seven years old. Luckily, we now have a genetic test available to screen our dogs. But in Samoyeds (and Siberians) PRA is an X-linked simple recessive trait. To understand how this works you need to have a good working knowledge of genetics. With most simple recessive genes, you just need to avoid breeding two carriers together. Not so with PRA in Sams. Because it is X-linked, you can never breed a female who is just a carrier, even to a tested clear male. However, you could breed an affected male to a clear female. Here is how it works.
The chromosome that determines sex are referred to as the X and Y chromosomes. A female is XX, a male is XY. When an egg and a sperm come together, each one has a half set of chromosomes. Each set finds its match and they zip them selves together so everything matches up just so. The mother always contributes an X chromosome. If the sperm carries an X, then the two Xs zip together and the puppy is a girl. If the sperm carries a Y chromosome, then the X and the Y chromosome zip together and you get a boy. Except notice that there is a portion of the X chromosome without a matching set of genes from the Y chromosome. When something is an X-linked trait, the gene is on this section of the chromosome.
When a female produces and egg and a male produces sperm, their DNA unzips itself again. (okay a gross simplification but this is the end result.) If you breed a female who is a carrier for X-linked PRA, half of her eggs will carry the X chromosome with the defective gene, half will carry the good copy. Then they get matched up with the male DNA, who is clear of PRA. Half his sperm carry an X chromosome and half a Y chromosome. The ones from the father with an X match up with the mother's X to make the girl puppies. Half the girls have a defective gene from the mother and are carriers. Half got the good gene from the mother and are clear. But none will go blind.
Now what with the boy puppies from that same breeding? Half have a defective gene from mom, half do not. But they are boys and have received a Y chromosome from dad. So there is no good copy of the gene to stop the disease from being expressed. So statistically half the boy puppies from the breeding will be affected with PRA.
Now how about breeding a male with the gene? Males can not be carriers, they can only be affected or clear. They have only one X chromosome and the gene is carried where the Y chromosome he has no corresponding gene. If you breed an affected male to a female who has been tested to be clear and not a carrier here is what you get. All the puppies who get his X chromosome get the defective gene. However, they will all be girls and get a good copy from mom. So all girls will be carriers. All the boy puppies he sires get the Y chromosome from dad, which does not carry the gene at all. So the boys are all clear. And no puppies will suffer from the disease.
Example number two from Samoyeds. The gene for dwarfism exists in our breed. Dwarfism comes with some serious and sad health implications and we really need to avoid it. For some reason, dogs who are carriers of the gene will have retinal folds as a puppy. This can be seen by a veterinary opthamologist if examined at the right age (about 8-9 weeks). Not all, or even most, retinal folds are associated with the gene for dwarfism, but some are. Retinal folds usually flatten out as the puppy grows. So say you have a female puppy you want to breed and she had retinal folds at 8 weeks but now has passed her eye exam, no folds. I would make sure to look for a sire who had been examined as a puppy and had no retinal folds.
I am only familiar with Samoyeds, but I am sure that every breed has their quirks. How do you find this stuff out? It's not published in any books, if you were lucky you could have learned about the PRA test from the optigen website. The folds/dwarfism link is not so easy to find. The only way you learn this kind of stuff is by hanging around with other Samoyed breeders, going to the nationals and the seminars at the nationals, being part of a discussion list for breeders of Samoyeds. In other words show breeders.
If someone is breeding pets and has and uses this kind of knowledge then I have no problem with them. Never heard of one though.