As an organic gardener, your best defense against disease and pest problems is a good offense. One of the strongest components of your offense is to grow vegetable varieties that are resistant to the pests that you have in your own garden. There are many vegetable varieties on the market that are tolerant of, or resistant to, various adverse conditions and pests. However, by breeding your own variety, you will be creating a custom plant that performs beyond compare in your garden.
Pick your Tomato Variety
Take your favorite tomato variety and decide what could make it even better (i.e. bigger fruits or better fruit set). You will be working to improve these traits.
Grow your parent tomato plants
Grow about 30 parent plants (you can grow fewer if you don't have the space--you will reduce your gene pool but will still get results). Arrange them in a block formation as opposed to a long row in order to get as much cross-breeding as possible.
Grow your parent plants at least 40 feet from any other tomato plants in order to keep them from cross breeding.
Pick your tomato seeds to save
After removing or 'rouging out' any plants that don't look healthy or meet your criteria, wait until the tomatoes become ripe and take seeds from your very best fruits--for example, the top 10% of the nicest fruits from the 30 % of plants that best meet your criteria.
After gathering your seeds, put them in a jar of water at room temperature until the seeds fall to the bottom of the jar. Then rinse the seeds until the water runs clear, making sure to discard any debris or seeds that float. You will then dry your seeds by spreading them in a thin layer on a cookie sheet or wax-coated paper plate and keeping them at room temperature.
By following these steps, you have most likely improved your tomato variety tremendously with respect to the traits you were selecting for. By repeating this process for another year or two, you can improve them even more and will have a 'customized' tomato variety that is distinctly different from the original parent plants.
One of the easiest and most rewarding vegetables to work with in developing your own variety or your own 'landrace' (a subset of a variety that is uniquely adapted to a certain area, including an area as specific as your garden) is the tomato. Tomatoes require a relatively small number of parent plants which enables you to maintain their genetic diversity by having a group of about 30 plants as opposed to about 1,000 for corn or 100 for broccoli. Tomatoes also have a relatively small isolation distance of 35 to 40 feet. This means that if you are working on developing a certain tomato variety (say a cherry tomato), you could have your beefsteak or canning tomatoes 40 feet away and they will not ruin your work by breeding with your cherry tomatoes.
Don't be daunted by this project even if you are a small home gardener. You're the expert on what grows best in your garden. Only you will know what you're biggest tomato growing challenges are. Cracking fruit? Late blight killing your plants? Poor fruit set when the weather is hot? Beautiful tomatoes with bland flavor? All of these are things that you can improve through breeding. So, if your favorite tomato variety has a taste you absolutely love but doesn't grow as well as you'd like or if you'd like to change the shape, size or flavor of it in some way, you can have your cake (or organic tomato) and eat it too!