Saving your Own Tomato Seed is Easy--Kind of...
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"1. You instructed us to let the tomato ripen beyond the verge of overripe. What's the basic science behind this recommendation?"
It's the most basic science, Tyler--the science of reproduction! When you save seed from your own garden (or from a purloined plant, not that I have ever considered such a thing) you want the seed to be as mature as possible. You can, for instance, pick a tomato at the peak of ripeness, enjoy the flavor immensely, decide to save its seeds and then get poor to no germination--because that tomato was ripe enough to eat but not ripe enough to reproduce.
Think about the original tomato plants in nature, growing at the base of mountains in Peru. With no humans to support them, the vines just....well, vined outward. Sometimes a bird or animal would eat one of the fruits, carry the seed to another area and maybe spread the range of the plant (again, if the fruit were overripe). But uneaten fruits would age to way-over ripe mushiness, their seeds would fall to the ground and many of them would give birth to new plants.
This is a great topic for this time of year, because the time to start planning to save seed is before you put any plants in the ground. First, you have to start with open-pollinated varieties. Hybrid plants are great in many situations, but not for seed-saving as they are crosses between two different parent plants and their children are unpredictable. Seeds saved from open-pollinated tomato plants will always produce the same type of tomato plant and fruit.
So let's say you grow THE perfect tomato and you know that it's an open-pollinated variety. (Hybrid varieties are always marked as hybrids.) Eat most of the tomatoes from that plant. Enjoy them. But resist the temptation to eat the most perfect tomato on this perfect plant. Leave it on the vine long past ripeness--until its practically falling apart, then bring it inside and dance the magic dance of Tomato Seed Saving:
Squeeze the juice and seeds into a medium size jar and add water until its three-quarters full. Let it sit out on the counter for three days, stirring frequently; it will get really grody looking. Then pour this skunk junk into a strainer and rinse the heck out of it. When there's only seeds left, let the strainer air dry for a few days, blotting the bottom with paper towels. When the seeds are super-dry, store them at room temperature in a sealed dry jar along with some of those desiccating pouches that come packed with vitamins and running shoes. Note: This fermenting process is only necessary for tomatoes; other seeds just need to be dried. Now, back to Tyler:
"2. I saved some seeds shortly before hearing your advice. The tomato was picked a bit underripe, it ripened indoors and then I cut it open for eating and saved the seeds. Can I expect these seeds to work or should I purchase new seed? (The variety is the heirloom Nebraska Wedding Fruit.)"
Try a germination test. Place some of the seeds inside damp paper towels, put the towels into a Zip-Loc bag but don't Zip it, and place it in a warm spot of your home. Make sure the towels stay moist. If the seeds spout after a week or ten days or so, you got lucky. If they don't, buy new seed.
"3. I grow many plants in close proximity (50 different tomato varieties last season). I'm concerned about crossing genetics if I save seeds. Do you believe that I can expect tomato seeds to be true, year after year, if I save them without taking precautions like bagging flowers before they open?"
Tomatoes do not cross-pollinate. Grow 100 different varieties, follow the directions I just directed and the seeds will 'come true' (except for hybrids, of course). The 'bagging flowers' thing you mention is to create hybrid varieties. Once the flowers open, you (the cross-pollinator) dust pollen from one variety onto the flowers of a different variety and then bag it to make sure no accidents happen. You make the right match and you got a great new hybrid tomato. If you bag flowers before they open, your chances of getting anything are poor to nil.
The garden crops that most readily cross-pollinate are pumpkins and squash. ('All pumpkins are squash but not all squash are pumpkins.') Some of the most common (and useful) native bees that hang around our gardens are the squash bees. They are incredibly promiscuous, moving from squash flower to squash flower without a care as to whether the flower belongs to a dipper gourd, butternut or acorn squash or a pumpkin.
This will not affect that year's crop. A butternut squash plant will still produce only butternut squashes and a Connecticut Field pumpkin plant will produce only pumpkins. But save the seeds from some of that year's squash and all bets are off. I once saved the seeds of a PERFECT pumpkin variety, planted them the next year and by August my garden was overrun with huge white gourds.