Yes there is only one original 'mother ' tree.
A breeder will start off with perhaps upwards of a thousand seedlings from a particular crossing.
He/ she then over several years gradually discards plants for a variety of reasons....poor growth,,,desease succeptabilty....poor cropping and lousy fruit...etc.
Eventually they will be left with just a few that they are pleased with. These will be bulked up by grafting and nowadays tip culture and the resulting trees sent out to various orchards to test them in actual growing and soil conditions and climate variations.
When these results are in then it will be decided if any of them are good enough for public sale.
Its a long process that usually takes about ten years or so.
The individual tree is then propogated up into a series of mother trees that go out to the nurseries for them to increase the numbers.
All the time though the variety can be traced directly back to the original mother tree.
Quite a process.
An apple a day.....keeps me in work.