I’m not a biologist, but I don’t think that is how DNA works. For one thing, there is no such thing as a “smart” gene. You cannot pass on being “stupid” genetically to your children, it’s impossible. Also, the African Masai tribe in Kenya and Tanzania has people that are very tall, and were tall thousands of years before Europeans came and took slaves.
It’s not one gene, it’s a combination of genes. Since stupid slaves were preferred (read Uncle Tom’s Cabin), they were more likely to be allowed to keep their kids. Since in normal populations a smart person is more likely to become rich and able to afford more children, after a few generations of freedom the balance should be able to go back.