Experimental Homestead

Apple Breeding part 3: From seed to fruit

lady williams seeds header

Seeds of Lady Williams. Some of them are sprouting inside the apple. So far it seems that fresh apple seeds sprout readily, and can be planted right away.



In part one I went over some reasons why I think home breeders have a decent chance of producing some good apples. Part two covered pollinating flowers to make intentional crosses of two different parent apples. In this section, I’ll discuss growing the seeds into seedlings, and options for growing those out until they fruit. COLLECTING AND STORING SEEDS:  I like to collect the seed when the apple is ripe for eating, but they seem to be mature before that.  I’ve stored the seeds in little plastic baggies in the refrigerator, but they sometimes mold.  Storing the seeds in slightly damp, but not wet, sand would probably be better, or you can just plant them… PLANTING SEEDS:  I’ve had pretty good luck with germination when planting in February after storage in the refrigerator.  At least some apples are supposed to require stratification, which means that they need to undergo so many hours of low temperatures before they will sprout.  I’ve had fresh seeds sprout without chilling, so I think fresh seeds just sprout easier.  My approach in the next years will probably be to store early seeds in the fridge in damp sand, and then plant them with the latest ripening seeds in February.  If planted outdoors, the seeds should chill enough as long as your climate is not subtropical.  If it is subtropical, then you should select seed parents carefully as many apples do not do well in warm climates with no chill.  The Apples and Oranges blog is a good resource for growing apples in low chill areas. It is possible to dry the seeds before sprouting them, but I don’t see any reason to do so when they can be kept in refrigeration, or even in the ground over winter. Plant the seeds in pots or flats, or outdoors in the ground, at about 1/2 inch deep.  Don’t allow them to dry out, but don’t over water either!  Over watering can lead to rotten seeds and fungal attacks.  One strategy I sometimes use is to put a growing mix in the pot or flat, followed by 3/8 inch of sand, followed seeds and finally covering the seeds with 1/2 inch of sand.  This method surrounds the seeds with clean aerated sand to sprout in, which minimizes bacterial and fungal attacks, while still providing them with nutritious flat mix just below.  My germination rate has been pretty mediocre, but since it doesn’t take long to produce a couple hundred seeds, maybe that’s Ok. apple seeds in flat After they grow a few leaves, you can move the seedlings outdoors into the soil, or into bigger pots.

These are on the young side for transplanting.

Most of these are on the young side for transplanting.

These seedlings are a little too big for transplanting. They would have done Ok regardless if I had taken better care of them, or put them into pots instead of in the ground. Better to transplant before they are crowded and when they only have a few leaves.

These seedlings are a little too big for transplanting. They would have done Ok regardless of that if I had taken better care of them after planting, or if I put them into pots instead of in the ground. Better to transplant before they are crowded and when they only have a few leaves, but things get in the way.

GROWING OUT:  Markus Kobelt at Lubera nursery gave me some tips on apple breeding.  He says that growing the seedlings as tall as possible the first year shortens the time to fruiting.  Seedlings are in what is called a juvenile stage.  Growing the seedlings fast and tall pushes them out of the juvenile stage and into sexual maturity more quickly.  My first batch of seedlings were left in flats for too long, and then planted in an out-of-the-way bed where they received poor care, resulting in some pretty stunted plants.  The seeds that I planted straight into the ground in a garden bed did quite a bit better.  Wherever you plant them, take good care of them with regular feeding and water.  Under ideal conditions you might end up with 4 to 5 foot stems.  Check out Markus Kobelt’s cool video series on all stages of apple breeding! It is probably best to cull some of the seedlings, but I’m not entirely sure what to look for in culling, so I’m not culling many of mine.  Nigel Deacon, in breeding for red flesh, selects for red pigmentation in the leaves as well as for vigour.  I’d like to talk to a breeding expert about culling.  At this point, I’m kind of cull shy. TO GRAFT OR NOT TO GRAFT?:  Is that the question?  I think a more relevant question is where to graft, because it is better to graft the seedling stems onto something else.  Putting the scions onto a dwarfing rootstock that encourages early fruiting, or onto a mature fruiting age tree will give you fruit sooner than growing the seedlings out until they begin to bear fruit, in some cases much sooner.  If you don’t know how to graft, or don’t have a mature tree to graft on to, you might want to just plant the seedlings and wait.  However, if you don’t know how to graft, now is a great time to learn!  If you come up with the best apple seedling ever, someone has to propagate it by grafting, so it might as well be you.  There are plenty of apple grafting resources on the internet and I’ll probably add my own before too long.

A basket of red fleshed apple seedling scions headed for dwarfing rootstocks.

A basket of red fleshed apple seedling scions headed for dwarfing rootstocks.  Note that each is labeled with the parents and a unique code so I can keep track of them all.  The original seedling roots have the same info and are being housed elsewhere in case of losses etc…

GRAFTING OPTIONS:  For the average home breeder, grafting onto a mature bearing tree may be the best option.  It requires a lot less room than growing each seedling on it’s own rootstock, way less care, and it’s cheap.  Rootstocks in small quantities will usually cost you $2.50 and up.  Larger quantities, usually 50 or more can get down into the $1.25 and up range, especially if you buy B grade stocks which have crooked stems.  Still, even at $1.25 each it adds up pretty fast, especially after shipping and handling.  Then you need room for all those stocks.  I’m planning to plant mine at 12 inches apart in rows about 6 feet apart.  All that sounds daunting, but there is one good reason to grow the plants on their own stocks and that is disease.  Apples are host to many diseases, but the concern here is with virus.  Seeds don’t carry virus from the parent, so the seedlings are virus free.  Virus are transmitted to a scion that is grafted to an infected tree though.  Most of us don’t have trees that we know are virus free, so keeping your seedlings fresh and unburdened by virus is somewhat compelling. The other side of the coin is that most apple varieties are minimally affected by the common Apple Mosaic Virus and there are millions upon millions of infected trees living and bearing fruit.  It is quite possible also that your mature apple tree is not infected anyway.  It is possible to rid a variety of virus by a process of heating, but that process is probably not accessible to the homescale grower (though I’m curious, maybe it’s not that hard!).  If having to graft onto individual rootstocks will keep you from experimenting, I’d say don’t let it.  Go ahead and graft them onto whatever you have. ROOTSTOCKS:  Very dwarfing rootstocks that keep trees under 10 feet will also induce fruiting early in the life of the tree.  I’ve mostly used bud-9, and this year some Geneva-11.  Geneva-11 has weak roots, so I’m not sure I like it yet, but the Bud-9 seems nice enough and it’s cheaper. M-9 is probably also a fine choice, though Bud-9 is generally thought to be an improvement on M-9.  Charts and descriptions of the various apple roostocks can be found online.  Just remember that you want one that induces early fruiting and makes for a small tree.  Trees can be planted close together in rows, I don’t think there is a reason to plant them further than 18 inches apart, and I’m probably going to use 12 inches to save space.  A trellis is necessary to support the trees since the dwarfing rootstocks lack adequate roots to anchor the trees in high winds.  Markus Kobelt says to let them grow without pruning to induce early fruiting.  I guess I’m going to follow his advice.  Don’t think of these dwarf rows as permanent.  They are more like shrubs for testing your new varieties.  If you get something good, it can be grafted and reproduced.  The original dwarf test plant is not important.  I have however saved the original seedlings which are planted about 6 inches apart in rows 12 inches apart… man is that going to be a mess in a few years!  I just wanted to save them at least temporarily in case of graft failures, gophers, accidents, etc…  Ideally I’d like to keep them all with enough space for them to grow and fruit later on, but that is not practical considering the resources I’m working with. I’ve gotten bulk rootstocks from both Copenhaven and Willamette Nursery, and have been happy with both companies.  Again, ask about B grade stocks to save some money.

Shaded nursery bed of seedlings on bud 9 and Geneva 11 dwarfing stocks. If all goes well these will be ready for permanent planting in rows on a trellis by next winter/spring. Note that I grafted the scions long. Not sure that was a good idea yet, but I suppose I'll find out...

Shaded nursery bed of seedlings on bud 9 and Geneva 11 dwarfing stocks. If all goes well these will be ready for permanent planting in rows on a trellis by next winter/spring. Note that I grafted the scions long, most of them full length. Not sure that was a good idea yet, but I suppose I’ll find out… (Edit:  Did they grow out?  Try ONE HUDRED PERCENT SUCCESS RATE on these grafts!  Goes to show, it’s good to question conventional wisdom and take risks sometimes.)

GRAFTING ONTO LARGER TREES:  Most grafting onto larger trees is done by a method called top working, wherein large branches are cut off, the cut is split open, and a couple of scions are wedged into the split.  That is a fast way to change a tree to another variety, but it is also crude and likely to introduce rot and disease into the heart of the branch.  Furthermore, it allows for very few varieties to be grafted onto the tree.  In Frame working by contrast, you work onto smaller wood, usually under an inch.  I avoid working into larger wood whenever possible.  If you use frame working, you are keeping the existing frame work of the tree, which has some advantages. I hope to blog about frame working sometime, and I’ll leave most of that discussion till then but, in the meantime, if you are working onto a larger tree, use scions with 8 to 15 buds.  Use cleft grafts if the branch is larger than the scion, and whip and tongue grafts if they are the same and you have a grafting skill level to do so.  I like to paint the longer scions completely with a thin coat of grafting wax to seal and prevent drying.  Other people use parafilm as a wrap to prevent desiccation of the scion.  See the Frankentree post for grafting photos.  On a large tree you can fit upwards of 200 different grafts, although if we follow Markus Kobelt advice to let the scion grow, that could get pretty messy, so leave plenty of room for each variety.  Albert Etter used frameworking to house the 500 or so varieties he collected for testing, as well as to fruit out and test the new varieties he was breeding. About 3 years ago I grafted 4 different open pollinated Wickson apple seedling scions onto various trees of mine.  They have grown great, but have yet to fruit out at all.  This season there is still no sign of blossoms at all on any of them.  So, this is a proposition that takes some time. My new seedlings have now been grafted onto dwarfing Bud-9 rootstocks and are beginning to grow in a nursery bed for planting out into a longer term growing site next winter/spring.  I grafted them rather long as that is my default any more, and it seems to work well as long as the graft is sealed.  Markus Kobelt says to graft the top of the seedling as it is less juvenile than the bottom.  In most cases I grafted most of the seedling stem, but then my seedlings were mostly well under 3 feet.  I also put 4 open pollinated red fleshed seedlings onto some larger trees to grow out for comparison.  I know I said not to use open pollinated seeds, but I just couldn’t throw the cute little things in the ditch!  Who knows what’s hiding in those genes. The grafted trees will be planted in rows at least 5 feet apart, probably 6′ feet on 12″ to 18″ inch centers and allowed to grow without pruning.  Allowing them to grow without pruning is supposed to bring them out of the juvenile stage, so that’s what I’m gonna do.  A trellis is necessary for support as these rootstocks are weak growers with small roots.  I hope for some fruit to examine and taste in about 3 to 5 years, but evaluating any that are decent enough to continue testing will be a much more lengthly proposition.  By that time I will have considerable investment in these plants, but the potential rewards are very exciting for an applehead like me.  Applehead, that may be the title of my next post… I’m also gearing up to make more crosses this season.  The list of interesting varieties is long but most, if not all, will be red flesh crosses.  I haven’t made a complete count lately, but I have over 200 varieties on trial that I can use as parents.  I’m just hoping I can curb my enthusiasm enough to keep my time investment low, since that is part of the plan.  A lot of people growing a few seedlings promotes diversity and keeps power in the hands of the people who eat the fruit.  a few people growing a lot of apples has it’s advantages to be sure, but to think that we will always be well served by such a system is naive because power is the primary currency of life, and consolidation opens the door for monopolization.  Breeding new apple varieties may not be the most important activity in reclaiming control of our food supply, but if it is a subject of interest to a person, it’s one pretty neat way to keep our food closer to home and to live dynamically with a source of our sustenance. If I can come up with one apple that is really worthy of propagation, something that will make people happy, I’ll be stoked.  That would probably be the most useful thing the Turkeysong project ever produces.  But the really great part that will make it all worth it, is that I get to name that apple whatever I want!  I’ve already spent way too much time dreaming up and listing prospective names.  So many names, so few apples… If anyone does come up with a good seedling apple, I just found this website which aims to promote seedling apples!  How cool is that… Seedlingapples on wordpress

April 11, 2013 - Posted by | Food and Drink Making, Food Trees Fruits and Nuts | , , , , ,


  1. Hello,

    I’m staring a bunch of open pollinated apples by mashing the cores and letting them ferment(3-5 weeks) as described by sepp holzer in his permaculture book. Any thoughts on his method? He grows a lot of apples from seed.


    P.s. found your website on cloudforest and it’s great!

    Comment by Hkai | April 11, 2013 | Reply

  2. It is interesting that the Lady Williams seeds sprout inside the apple–Kevin Hauser says that’s also true for Cripp’s Pink, which is an offspring of Lady Williams. So the “seed precocity” may be inherited. Now, Lady Williams is an offspring of Granny Smith–does Granny Smith have seeds that sprout in the apple? Some folks think that Lady Williams’ pollen parent may have been Rokewood, an Australian apple that isn’t well known, but which, like Lady Williams, is an extremely late ripener. Perhaps Rokewood is where the seed precocity comes from.

    Since my last comment on your previous post, I have started thinking that perhaps the best way to think about the efforts of amateur apple breeders is by analogy to distributed computing projects, where people lend time on their home personal computers to huge scientific computational projects. Chances are slim that your computer will find the solution, but chances aren’t too bad that somebody’s computer will. Likewise with apple breeding–maybe you won’t be able to grow enough seedlings to find the next great apple, but if a few thousand people all planted a hundred seedlings, 10,000:1 odds no longer look so discouraging.

    Comment by Michael Schmidt | April 14, 2013 | Reply

    • I think I had another variety that was sprouting in the apple, but can’t remember for sure. I’ll look into Rokewood. I’m always looking for extremely late apples. Granny smith is supposed to be descended from the French Crab, so there’s one more step to follow back looking for that trait.

      Yeah, I had conceived something like that too, where a large number of enthusiasts are all working toward the same goal, which is to keep more improved and diverse types of apples coming into the public domain. Various people might be able to take up different parts of the work. I know it’s not too hard for me to produce seeds and grow a bunch of seedlings, but I can only grow so many out with the resources I have. I can see potential problems though. Evaluation would be an issue. Evaluation would take a long time and probably more apples would be kept than really should. Like one of those Pacific Rural Press quotes said “Then also, the joy of discovery of new varieties evidently warped the judgment of many discoverers, and an astounding proportion of the 500 named varieties grown are of as little merit as apples well could be.” I think anyone could fall prey to that blunder. It’s a really cool idea though if someone could organize it all and make it happen.

      Comment by Stevene | April 14, 2013 | Reply

      • “Then also, the joy of discovery of new varieties evidently warped the judgment of many discoverers, and an astounding proportion of the 500 named varieties grown are of as little merit as apples well could be.” Yes, that is certainly imaginable! I’m sure I will convince myself that the first halfway decent seedling I taste will be the best thing ever.

        I wasn’t thinking really of an organized effort–but a haphazard one in which lots of people make lots of crosses and evaluate them on their own. Which is essentially what has occurred throughout the ages. The difference now is that there is much more organized discouragement of amateur breeding and selection–which simply needs to be countered by enthusiastic encouragement. “Yes, you are likely to be disappointed by the results, but you will have fun trying, and you may get lucky.”

        Comment by Michael Schmidt | April 15, 2013

      • I had a store-bought Granny Smith the other day that had sprouting seeds, so that may be another step back in tracing that trait….

        Comment by Michael Schmidt | April 25, 2013

  3. Upon further thought, an evaluative method based on internet marketing models might actually be an improvement over the traditional. One person’s favorite is another’s skipover. But think how marketing on amazon works–if you like x, you are likely to also like y. If you can grow z in your climate, you will probably also be able to grow q. Leaving aside the supermarket issues for now, imagine the scion network of the future. I create five varieties that I like, and that do well in my climate, and I can give scionwood to others who have similar likes and dislikes in fruit characteristics, and who grow apples in similar climates. Much better, it would seem, than a few big nurseries deciding which 12 varieties everyone will grow. Eventually the varieties that appeal to the broadest populations will be the most widely planted, and they’ll find their way into local farmer’s markets and maybe even supermarkets and commercial orchards. The only problem, if it is that, is that nobody will get rich off of developing the variety.

    To make this work, there need to be enough enthusiastic small-time growers to fill the database with enough correlations to start making reasonable recommendations. OrangePippin.com is a step in that direction, but they aren’t really pushing the data harvesting and mining that is possible.

    Comment by Michael Schmidt | April 15, 2013 | Reply

    • Neat ideas. I think the internet has the potential to take power out of the hands of large scale suppliers and marketers of things and allow small things to grow big on their own merits via word of mouth so to speak. We’ll see how it plays out though. The explosion in interest in apples is largely due to internet communications. I would hardly know anything about the varieties I’m growing without the internet… actually, I just wouldn’t have them. I’d like to see more breeding going on for altruistic reasons and released directly into the public domain, and the internet has great potential for getting those varieties distributed, tested and generally popularized.

      Its rather disturbing that a lot of trees are sold without much regard to whether they will really do well in a given area. They can expand the list of varieties that are broadly adapted, but that still just leads to less diversity overall. That’s why I’m testing so many varieties here.

      Comment by Stevene | April 15, 2013 | Reply

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