Most seedling apple trees grow to a standard height of 16 or more feet, with no guarantee they will bear edible fruit. In those not bearing edible fruit, disease resistance may be lacking and some seedlings may be sterile. Other trees bear unusual and valuable new strains of fruit. Any seedling that reaches whip size serves as rootstock for grafting scions of known varieties.
Collect seeds in the fall from the cores of an apple strain known to grow well in your area. In the wild, apple seeds undergo a long period of winter weather before sprouting. Seeds that do not experience this long winter chill will not sprout. Stratify seeds by placing apple seeds in damp peat in a Ziploc bag and storing the sealed packet in a refrigerator until spring. Cold storage for two to three months should be enough. By spring, many apples stored over winter contain stratified seeds.
Plant the apple seeds indoors in peat pots a few weeks before the last spring frost. Bury the apple seeds 3/4 inch deep and place the pots in a warm location like a southern-facing window. Keep the peat pots moist. When seedlings emerge and first leaves form, begin hardening off the plants by moving them outdoors for a few hours daily.
Transplant the apple seedlings--still in their peat pots--to a fenced garden as soon as all danger of frost is passed. Space seedlings 3 inches apart in the row if using the trees as rootstock for scions. Deer or rabbits could graze the seedlings to the ground if the young trees are not protected.
Collect vigorous pencil-size scions of known apple varieties for grafting to the seedlings later in mid-winter. Cut the scions after the leaves fall and store the grafting stock in damp layers of paper towels inside plastic bags and under refrigeration until needed.
Dig the seedlings in February while still dormant. Protect the roots from drying out during the grafting procedure. Begin whip grafting by making a long diagonal cut through the seedling 2 inches above the roots. Make a matching diagonal cut in the base of a scion of about the same diameter. Tie the scion to the seedling with a wrapping of rubber bands or grafting tape, and paint the junction with pruning sealer. Place grafted seedlings in moist peat and keep them in cold storage at 45 to 50 degrees F until spring.
Plant the grafted seedlings in permanent locations in April. Plant to the same depth as before, being careful to lift the plants only by the rootstock and never to bump the scion. Jarring the graft could break the connection forming between scion and seedling.