I made a post recently to share my experience growing apples from seed, and I thought it would be good to make it an article here. If you want to read the full thread and related topics you can find it here.
The same methods would work for many other perennial seeds to get them growing early and have transplants ready in the spring. Another reason to do this is therapeutic, there's value in the sensory experience of having a winter garden and spending time under the grow lights and caring for plants during the short winter days.
For the past couple of winters I've started apple seedlings indoors to get a head start on the season. These are usually Malus baccata, I grow them for rootstocks. If you're thinking about growing apple trees indoors, I can briefly describe what's worked for me.
The seeds I'm growing this winter are from apples collected in September, the seed was cleaned and dried overnight in a dehydrator on low and then stored in a fridge. Will skip those details, apple seeds are orthodox and store well if dried and kept cold.
Around the end of December is when I start stratifying seed, and I give them 5-6 weeks in a cold fridge. Seed is soaked in water for a while, this year I also soaked them in a 10% bleach solution for a few minutes and rinsed. To stratify them put the seed in a ziplock bag with a few tablespoons of slightly damp sand, label, throw in fridge. I started 500-600 seeds this year, which was maybe a gallon of 1" crab apples.
Mid February the seed is ready to get planted. I've tried earlier and later, this seems to be good timing. Note our last frost date here is the end of May.
So a few days ahead of planting if the grow space hasn't been setup for the winter yet, I'll wipe everything down to sanitize it including any tables / shelves, all the pots and trays I might use, areas with potting medium, sweep the floor etc. I have a space that's maybe 10x10 in a spare room, it's enough room for 6 lights and 25-30 1020 trays, and often I'll get creative and do a 2 tier shelf or hang a light under a bench to get more area. The reason for keeping things clean aside from the obvious is that pests including insects, mites, mealy bugs, aphids, and fungi like scab and other fungus issues are best avoided with sterile everything and good horticultural hygiene, they love to setup shop in an indoor grow if you bring in soil from outside, or even from a plant brought in from a garden center, a houseplant put outside for the summer, etc. I'll clean and sterilize any pots or trays used before with a dilute bleach solution and soap.
When I planted in past years, I would start seeds in a tray just broadcast and then prick them out over the next couple weeks. This can work, you just want to be careful not to J root them, use a dibble. You can also germinate them in damp paper towel for a week and then carefully plant them as soon as there's a radical. If I know that my seed will have a good germination rate, and I have all the trays and potting mix on hand, I like to direct sow them into cells. Last year I started in small cells like 128 and 200s, and then after they got up to size at six weeks were transplanted into 50 cell trays. This year I'm going to try direct sowing them into individual 2.5" pots. I started using these in the greenhouse this year for rooted softwood cuttings and prefer them.
So I'll fill up a bench with 1020 tays each with around 32 of pots (4 rows of 8 pots) and I can fit 16 trays on an 8 x 3.5' table. The trays are solid for bottom watering. I hang 3 led grow lights over that space about 18-24" up. The trays stay covered with some plastic lids or at least misted daily until germination. This is a precarious time for seedlings because of damping off, so I'll turn on an oscillating fan across the room to keep up good airflow and try and get the top layer of soil / potting mix to dry out mid day. The fan stays on for the whole grow, if you can get it to move the leaves a bit it makes the stems stronger.
I keep a google sheet on my phone with some notes and dates through the grow, this is useful if you're going to do it again. Btw try and google data like that, seedling growth rates etc for small trees, can be tricky to find. How big can the seedlings get by spring? In my experience it largely depends on the container size, given adequate light and nutrition apple seedlings growing indoors seem to grow faster than outside, maybe it's the constant air temperature. They can put on about 1" and one new leaf per week.
I'll grow them for 3 months and then move them outside to my greenhouse during a week with nice weather, and set them on a bench under shade cloth to harden off. I leave them in the greenhouse for about 3 weeks, working to avoid shock. I'll run a heater in case of frost but I find so long as they've hardened off for a week or more a light frost doesn't affect them. I'll put them outside during mild weather after the last frost, and I like to set the tray on the bed and leave them for a few days or a week to acclimate to their first real experience with full sun, temperature, wind before planting. Hardening off can be done in smaller steps, but moving 25 trays outside for an hour then moving them is, 2 hours the next day, etc has logistical issues. I use shade cloth and try and make environmental changes as small as possible, then at least a week before another change. One year I planted them during a hot sunny day and nearly killed the whole lot, they wilted and browned off most of the leaves, and then they regrew their leaves after some weeks but it set them back. I had a few that stayed dormant the whole rest of the season - it was a good lesson.
I plant them into nursery beds with 6"x12" spacing, so a 3' x 20' bed can fit something like 200. Wider spacing probably will give you bigger trees. I use lots of wood chip and compost, and water them regularly when there isn't rain. By the end of October here the leaves drop and I can lift the whole bed and group them into bundles, and at this point grade them if any are too small they get planted out for another year, the rest are good for spring grafting. If you were growing on the seedlings you could plant them in the permanent location the first fall, or heel them in for spring. If you did some controlled crosses you could take a good sized scion after the first season. If might be possible to t-bud them the first fall, especially if your growing season is a month or two longer than here.