There are 13 wild tomato relatives that can be crossed with domestic tomato. Embryo rescue is necessary with about half of them. That means you are starting with 14 separate genomes, some of which have more diversity than all of the others combined. (S. Peruvianum) When you combine all of them into a single plant, you have of necessity limited yourself to 2 specific genomes. Selfing that plant will cut you back down to 1 genome. So from 14 highly diverse genomes the result is a single genome with most of the diversity lost along the way.
As Darren Abbey said above, the way to increase diversity is to include as many breeding groups as possible. The more plants in the interbreeding population, the more diversity retained.
There are lots of genes that should be eliminated. For example, S. Habrochaites has a huge cold tolerance gene on chromosome 12. Domestic tomato has very little cold tolerance. It makes sense to eliminate the chromosome section from domestic tomato and keep the one from S. Habrochaites.
|