I have a mare with nice conformation, a very good and big mover, nice large pony size, mid-teen, and has most likely has been shown in-hand and had foals (several reasons I think so). Problem is, I have NO idea exactly her breed or history. No brand, no papers, nothing. Are there any registries that require DNA testing, giving me the option to send in some of her DNA just to see if she's registered? Obviously not registries like AQHA, AMHA, etc.
Next, are there any GOOD breeders that have mares with unknown histories/pedigrees as their broodmares? Not including backyard breeders that breed their grade mare to a Paint x Appaloosa x Thoroughbred x Shetland, or breeders that have a random nice pony mare that did the division ponies for 8 years before breeding her (my pony has no performance record under saddle).
The registries can only test against specific horses, not just run her DNA through their database and see if she matches someone. If only that were the case! Have you tried checking her for a microchip?
Parentage verification is done by comparing DNA markers from the horse against DNA markers from the reported parents. They must have some idea of who the parents are (or at least one parent), so they know whose report to test against. And the parent's DNA must already be in the database, or else you have to furnish the parent's DNA sample. They can provide up to 99% certainty on parentage with reports from both parents, or up to 95% certainty with a report from only one parent.
Also bear in mind that every test costs money - to run a horse's DNA against every horse in the database would probably cost thousands of $$$. And I'm not sure they would even do it, as it would be very time-consuming and would tie up their equipment and personnel.
As to whether the good breeders use "unknown" mares - probably very few do. Breeding is such a crap shoot even when using "known" parents, it doesn't make sense to use an mare with unknown genotype.