I was shocked recently to find that all of the apples that we buy in the supermarkets, they are all hybrids of hybrids of hybrids, and if you grow an apple tree from seed, it will never be what the parent fruit was because there is no wild left in it, it is all hybridized by grafting on non fruit dwarf tree stock, or most of it is dwarf anyway.  I thought other rose family members were all true to seed, who knows maybe they aren't as well.  So, in my reading over the last few days, it occurred to me, if you happen to be lucky and get a nice apple, say maybe even better than the parent, you grew it from seed, won't those seeds be true to seed?  I'm real curious to know what experience others have had on this topic because I am starting to become bothered thinking about all the fruits that I really like so much (Braeburn Apples have to the the tippy top of the list) are dependent on someone performing that grafting thing. What happens after a nuclear winter (as an example)? We won't have any possibility of having Braeburn Apples ever again   What a bummer that would be. So I am very interested in hearing from others that had positive experiences with growing Apples from seeds.

I think it depends how far down the rabbit hole you want to go.  Realistically, breeding apples for certain characteristics that humans desire is unnatural.  Plants will always cross with other cultivars within the same species and hybridize, given the chance.  In nature populations of tree in any given area would be likely to have quite similar genetics, since they have the same evolutionary pressures on them and have spread from the same genetics.  But if one population of trees grew close to another, different population of trees in nature, they would hybridize.  So what is more unnatural is really the fact that there are all these different apple varieties we've bred, not hybridization itself.

Grafting is a separate issue - it is really just a way to propagate the same genetic material.

Dwarfing is another separate issue.  You can graft an apple tree onto a non-dwarfing tree.

There may also be hardiness benefits to raising trees from seed in situ (even if you graft other varieties onto them), as they can then form a taproot, whereas transplanting damages this development.

Any apple you get anywhere has a chance of not growing true to seed, unless it has been grown only around other apples of the exact same genetics.  It's a bit like your pumpkins in your veggie patch, you could end up with a dud if you let them cross pollinate.  From what I have read you have a fairly good chance of getting an edible apple from your seed, but if not you can always graft another cultivar on.  And the child seeds of your tree will be different again depending on what they get cross pollinated with.

In trees it is easy to cultivate wanted varieties through grafts, and this can be done by the home gardener in a nuclear winter if need be.  Hybrid seed for veggies has quite a different production process where plants are grown in controlled conditions and the male organs of some of the plants are removed by hand so that they do not self pollinate, allowing the second variety to pollinate instead.  This is often done in third world countries like Taiwan, where labour is cheap.  Arguably it is not worthwhile without cheap labour, so in the future hybrid seeds may become far more expensive.

Many types of plants (as well as human beings) do not 'breed true' - the offspring are not exactly like their parents for generation after generation, each individual can have unique characteristics. This is both good and bad.

In terms of apples, the original apple was small and sour. It took many generations of selection to get the fruit to be large and sweet and have the texture that makes it most appreciated by humans. We did 'breed the wild' out of many fruits and vegetables in the sense that we chose plants with larger, tastier edible parts. And as a side effect, these plants may lack the things that protect from pests in the field (thorns, stiff hairs, bitter alkaloids, high levels of acidity, anti-nutritional factors, etc). In a world without humans, the braeburn apple and the cocker spaniel dog would not exist.

You can plant apple seeds, but the children are not exactly like the parents. Without some program to select and breed apples, they would revert to the wild form - after a few generations, the plants would have smaller, sour fruit - many of the first generation of wild would be noticeably different, after a few generations, most apple trees would be like crab apples. That might be ok for people that wanted to press cider, but not so much for having fruit to eat out of hand.

http://www.permies.com/permaculture-forums/998_0/permaculture/growing-apples-from-seeds-vs-cloning

Thanks Paul, I knew there had to be a discussion on this already, but how to find? Thanks! Looks like you had the same questions I had too which got me going down this road (tap roots).

Johnny Appleseed grew apples from seed at his nurseries, but he was selling apples mainly for use in cider orchards, not for fresh eating.  Other nurserymen sold grafted apple cultivars for the fresh eating/pie market.