I have changed quite a bit about how I store and germinate seeds and grow seedlings. I definitely do not have this all figured out. There are a lot of options to choose from, depending on climate and resources. I’ll tell you what I’ve done and what I’m doing now.
I used to put the fresh seeds into the refrigerator to sprout in a damp medium. I would also store fresh seeds in small zipper seal bags to sell later in the winter. At some point, I decided to dry seeds, because sometimes I’d have mold in the bags. I found the germination seemed better in seeds that were dried, then re-soaked, so that is what I do now. It is also much more convenient for storage and sale of seeds. Dry seeds allow a lot more leeway in when they are planted and can even be kept over for the following year. I’m not sure how long they last, but probably a few years at least in decent storage conditions.
Apple seeds need cold stratification, also known as vernalization. Apples originate from cold climates and the way they know it is time to sprout in the spring is when they have been cold for a while. This process can happen in a fresh seed, or a seed that is dried and re-soaked, but not in a dry seed. If seeds are dry, either re-soak them overnight, or plant them in damp soil and they will take care of rehydrating themselves.
Your two options are basically to stratify in the soil where it is cold, like outside, or in an unheated garage etc., or to stratify in a refrigerator before planting. These methods can also be combined of course. I’ve had the best luck so far by germinating in pots outside. We have enough chill to easily take care of stratification if they are planted by early winter. In a colder climate, I would be thinking of maybe putting them in a garage or the like, where they will not get extremely cold, but cold enough to stratify. You could also stratify in a refrigerator for the winter and plant in the spring or as they sprout in the storage bags.
Either way, avoid getting them very warm before they germinate, or they can go into a secondary dormancy. Temps in the 70s are great for germination, but into the 80’s and above may stall them and you’ll have to wait until the next year to start over. Once the sprout, you can put them in a warm area to grow. It is just getting them to sprout that is the trick.
For large plantings of random seed, such as for growing a bunch of rootstocks, you could sow into an outdoor bed, but for valuable seed that is a pretty risky approach. I’m using Anderson tree bands that are about 2-3/8” x 5”. These are like pots, but the bottom is mostly open. They fit snugly into a plastic tray made for them which has a mesh bottom. This is a space efficient system that is easy to manage, but requires some investment. Anderson pots and bands are also not widely available. GrowOrganic website has decent prices and shipping, but they don’t carry the big square heavy duty trays. Steuwe and Sons carries most of the anderson line, but shipping can be more than the pots. Anderson themselves sell wholesale only.
Most can get away with scrounging up some random small pots. Most pots are made to fit in the common standard 2 inch deep nursery trays, and or 10/20 trays. For a larger project, anderson bands might be worth the investment. They are really nice and very durable so they can be used over and over. I inherited a bunch, but I have bought some too for certain nursery projects and will probably invest in more and more trays. They are a very space efficient and convenient system for situation where the same pots are used year after year for nursery work. Pots are all made in fractions of each other, like 1/2, 3/4, 1/3, 1/4, so that they will fill out the same tray system.
The advantages to pots are many. If the pots are in trays, it is easy to move and manage them. Try moving hundreds of little pots that want to fall over, vs a few trays. 36 of the pots I’m using now fit into the 15 x 15 inch Anderson trays. Each tree gets to grow its roots without competition and can be planted out with minimal root disturbance. If the seeds don’t sprout, they can be allowed to dry out and the pots stored for the year to see if they sprout the following season, which they not uncommonly will. My best year ever for seedling growing was last year, when I planting into these small pots by mid winter and leaving outside to stratify naturally. There were still quite a few pots that did not germinate, but I saved them and we’ll see how many come up this year. Those plants also performed well after transplanting for the most part.
If stratifying in the refrigerator, I prefer to put the soaked seeds into a medium. I’ve used wood shavings, charcoal, potting mix and crumbly rotten wood from old logs. You can use anything along these lines, but make sure it is damp and not excessively wet. I would avoid any kind of paper though, as it often grows mold much more easily than natural materials. If you use zipper lock bags, they should not dry out at all. You can either wait until the seeds actually sprout in the bags, or keep them cold in there for a while, then plant out in a cold area.
All in all, I’ve had patchy results with germination. I suspect that is just how it is with apples. Some varieties and species probably require much longer stratification times. I have noticed some crabs and crab hybrids show poor germination. They probably just need especially long cold stratification. Just try to give all of them the longest stratification time you can before the weather gets really warm. Avoid putting them in greenhouses before they are sprouted, unless it will stay in the mid 70’s and lower. One thing I read basically said that they will germinate faster when it is warm (up to a limit), but more reliably if slower in the 40’s.
If you have grow lights, you could sprout them under those, either in a cold garage or similar spot if they have not stratified or sprouted yet, or indoors at room temp if they are already stratified well or sprouted.
I would say minimum cold stratification time should be 6 weeks, but more is probably needed in many cases. If using baggies in the fridge, you can look through them once a week and plant any that are sprouting. Even the slightest root tip emerging is enough to know they have broken dormancy. This is not an exact science. There seem to be a lot of variables at play, some of which we probably will not ever figure out. Producing extra seed when you can to offset germination failures and planting in pots so that you can hold unsprouted ones over til the next year may be about the best expedients we can come up.