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The Science of Grafted Trees

by Elmer on 03/13/2012
apple seeds

Have you ever wondered why you can’t just pull out the seeds from an apple at the store, plant them, and grow trees that yield the same exact apples you originally took the seeds from? To answer this, we’ll address the history contained in seeds as well as the benefits of planting and growing grafted trees.

Reproduction in Fruit Trees/Nut Trees

We’ll use apple trees for example here. Most apple trees are not self-fertile; they need another apple variety to pollinate the blossoms and produce fruit.

So, if you had a Honeycrisp™ apple tree, you would need a variety like the Golden Delicious apple tree to cross-pollinate it. From one tree to the other, the male flower’s genetic material pollinates the female flower (usually helped by bees, wind, etc.). The end result is fruit development in mature apple trees.

This is called “sexual reproduction” in trees. And, even if a tree is considered to be self-pollinating, it’s still receptive of other pollen — so the seeds of its fruit will contain a family history of generations of trees.

The combined genetic material of a tree is in the seeds, not the fruit. This is how cross-pollination can occur in your Honeycrisp apple tree and not affect the color or appearance of the apples. The seeds, however, carry the traits of the tree’s pollination partner (Golden Delicious, in the example above), plus the genetic history of all past generations of both trees. So, If you were to plant a Honeycrisp apple’s seed, the resulting apple tree could display characteristics from anywhere in its lineage. It will not be a true Honeycrisp apple tree or bear true Honeycrisp apples.

Plant Breeders

There are exceptions, like certain citrus trees, but most seed-grown fruit and nut trees (seedlings) are unreliable if the goal is consistency. Even when deliberate crosses are made by plant breeders, the results in the offspring are unpredictable. Breeders select the most promising characteristics from parent plants and allow them to cross-pollinate. Then the resulting fruit’s history-containing seeds are harvested and planted to grow the next generation of trees. These trees bear fruit that (hopefully) outperforms the parents. It is said that the late great plant wizard Luther Burbank made 700 deliberate crosses of Orange Quince and Portugal Quince just to produce the Van Deman Quince!

Grafted Trees

Then there are grafted fruit trees. Grafting involves taking a scion or bud chip* cut from the desired parent tree (say, a true-to-name Honeycrisp Apple tree) and literally placing it onto another tree or a compatible rootstock. The grafting piece (scion) and the rootstock are calloused, or knitted, together as it heals. All suckers are removed from the rootstock, and the Honeycrisp scion is allowed to grow into the new tree, thus maintaining its true identity. This process is called “asexual reproduction” (apart from sex). Since only one parent/variety is involved in this process, the grafted tree will be true-to-name. And a true-to-name tree bears true-to-name fruit!

*Most Stark Bro’s trees are either propagated through grafting — by splicing the scion and rootstock together — or through budding a single vegetative bud into the side of the rootstock and wrapping it with cellophane tape until it heals. The results of grafting and budding are the same.

Variation vs. Consistency

So what’s the practical difference between a grafted tree and a seed-grown tree?

Seed-Grown Trees

We’ll use seed-grown nut trees to demonstrate this example. If you were going to plant 10 pecan seedlings or black walnuts seedlings, these may be the results:

  1. They could all have varying growth habits (some fast, some slower).
  2. There could be several weeks between the different trees’ ripening/harvest times.
  3. Some trees might bear in 7 years, others might bear much later.
  4. The size and quality of the nuts each tree produces will vary.

In short, you really don’t know with certainty what the outcome will be with a seed-grown tree.

See the variation (leaf size, shape, etc.) in these native, seed-grown apple trees?

Apple Domestic Seedling A Apple Domestic Seedling B Apple Domestic Seedling C Apple Domestic Seedling D

Grafted Trees

A grafted tree is consistent, with a reliable history of characteristics. It has a track record!

  1. It blooms at a certain time.
  2. It bears fruit at a certain time.
  3. You know whether the tree bears early, is disease-resistant, or has other unique traits.
  4. You can expect the fruit to be a certain size and quality, i.e. true-to-name.  (“A tree is known by its fruit.”)

See the consistency in size and shape of these grafted trees?

With this in mind, I will always recommend you plant trees that were propagated through grafting or budding methods. It’s worth the investment to know exactly what you’re getting!

– Elmer

Topics → Tips


  1. Bina J Hutson permalink

    Well, this is the 8th year for my “grafted” Honeycrisp tree purchased at Stark Bros, and I have only had 1 year that produced a handful of apples. We have done everything right. Fertilize, prune and use Gold Rush as a pollinator. The Gold Rush tree, purchased at the same time as the Honeycrisp is very prolific. Can you tell my why the Honeycrisp tree does not produce apples? My husband wants to cut it down.

    • jeff permalink

      its possible there have not been enough cold winter days in your area for that variety to produce well and the pollinator may be able to produce a good crop with less freezing days.were the apples honey crisp when it did produce, other possibility is root stock grew up and graft died.

    • Austin McKinley permalink

      You might take a soil sample to your local fertilizer plant, for your soil might lack in nutrients.

    • Hello Bina. Jeff & Austin provide good information here! It never hurts to know what nutrients might be lacking in your soil. Chill hours are important in fruit production, especially the Honeycrisp which is more of a cold-tolerant apple tree.

      Another thing that may have happened is your Honeycrisp is receiving too much nitrogen from fertilizer. Each tree is different so one tree may respond differently to the same care you give another. Nitrogen encourages green-growth in a fruit tree and this can result in little to no blooming on a perfectly healthy tree.

      Before your husband cuts the tree down, I would suggest holding off on fertilizing this year and avoid any “hard pruning” (this will encourage vegetative growth as well). Prune about a third of this year’s new growth when it comes time to prune (late fall/winter).

  2. Janet Mixon permalink

    Do you offer a service of grafting trees for your costomers. I have a pear tree that I love, but it is on the downhill slide. I would love to have this tree propagated. Thanks, Janet Mixon

    • I’m not affiliated with the site, and I have no idea if they do grafting services (that seems like something that a local nursery should take care of), but I had something like this come up with a fig tree this year. You may want to consider making a cutting and rooting it. There’s a ton of info out there about both doing your own grafting and rooting cuttings. I use bottled rooting hormone, myself, but I really want a willow tree so I can produce my own. In your place, I would try to raise both a root cutting and a tip cutting in order to make the same kind of graft as the plants grow. I currently have something like 8 or 10 little fig trees starting from my now deceased parent plant. Good luck with your pear tree.

      • Nef, please, tell me how to make rooting hormone from willow trees, or how to use the willow tree in doing this.

    • Hi Janet! This is not a service that we provide customers but I do think that if you check with your local county extension agent they will be able to connect you with someone who does provide this service in your area.

    • Peter permalink

      I personally don’t consider grafting to be the same thing as propagation, although there are many people who consider grafting a form of propagation, and most plant propagation literature will discuss grafting. Anyways, I consider grafting a type of tree augmentation and propagation as producing new plants from parent plant material.

      Anyways, it sounds like to me that you’re trying to get a new pear tree from the one you have in your backyard so you’ll have to learn a bit about both to do it properly, although if you only want to change the pear tree variety, you would only have to graft it.

      Here’s a guide on grafting from North Carolina St.( If you’re trying to change your pear tree variety, then focus on the cleft or bark graft. The next four grafting methods after the cleft and bark graft (side-veneer to saddle) are the ones you should focus on if you’re trying to duplicate the pear tree you have. You’ll need to find a rootstock then graft your scion (which in this case will be your pear tree) onto it. I don’t know if Stark Bro’s sell one year old rootstocks to people, but you should contact your local extension on what rootstock to get and find a reliable dealer (like Stark Bro’s, I went on a field trip to their facilities last year, and Elmer Kidd, their production manager, really knows what he’s doing; he told me when he was younger, he could do thousands of grafts in a day). You should also identify what pear variety you have because there is graft incompatibility between some varieties, and grafts between these varieties will not heal properly.

      If you don’t care for a rootstock (which basically means you’re giving up disease resistance and any control over the size of the tree), then you can take a 6-8 inch branch cutting from your tree, strip the lower 1-2 inches of the bark (be sure to leave the green layer underneath though, this is the part where the plant cells actually divide so they’re needed to form roots), dip them with some rooting hormones (or don’t, they just increase success rate), and plant it into some grow media, potting mix, or soil. Whatever you plant it in, make sure it’s kept moist, but the plants will still need air to form roots, also, if you’re planting them in the soil, they may require some treatment to make sure fungal root diseases don’t develop along with some covering to keep the humidity high. You also have the option of air layering ( to get new pear trees. Which ever way you chose to propagate your tree, you should do it during the first half of the growing season before the tree begins to fruit then harden off for the winter because this ensures that the branches used for these propagation methods will have the resources to produce roots. Otherwise, during the flowering stage, all the plant’s resources are going towards the flower, and then the plant diverts its resources to the trunk and roots to overwinter.

  3. Bobby Robinson permalink

    I have 4 pear trees on my property located approximately 20 feet apart. Three of them bloom and produce pears every year. They are all about 8 years old. One pear tree grows well but never blooms or produces fruit. What could be the problem. I trim the trees in February every year.

    • That’s not uncommon, Bobby. Sometimes when this occurs, it is helpful to stop applying fertilizer for a year (if you use it) and also try Root Pruning.

      In the Fall, go out to the tree with a shovel and walk off the trunk of the tree out to the end of the branches. This is referred to as the “dripline” of the tree.

      Take your shovel and sink it all the way in the ground, remove the shovel but do not remove any dirt. Push it straight in and pull it straight back out. You are making a slit in the ground to cut off some of the feeder roots. Move over a couple of feet and make another slit and continue to do this all the way around the tree; creating a dotted-line circle.

      It will stress the tree, but will not kill it. This procedure discourages the tree from growing too vigorously and will encourage it to put on fruiting blossoms the next spring.

  4. Howard permalink

    I too have a Honeycrisp that has never flowered despite other trees that are abundant. I have successfully grafted some of the Honeycrisp onto a very prolific Fuji in an attempt to at least force some fruiting potential. And my original Honeycrisp does not have a failed graft. The tree is healthy, but barren.

    • Howard I would suggest holding off on the fertilizer for a year if you use it on your Honeycrisp apple tree and it might benefit from root pruning as well.

      Honeycrisp is recommended for areas between zones 3-6 which is typically ideal for its hardiness as a tree and chill hours for its fruit production. Is your area zoned in that range?

  5. Howard permalink

    Hi Sarah, thanks for the prompt reply. I’ll try the root pruning. I’m in zone 8, but normally I get enough chill hours to satisfy. I’ve even pulled branches down to horizontal to attempt a stimulus. But nothing.

    • Alright, well, definitely give the root pruning a try, Howard, and keep us posted! :)

  6. Greetings…

    I really liked the little info on the grafting… most I was already aware of, but liked anyway. I was really surprised the first time I heard this info, and feel that more people would like horticulture if they knew there was more to it than meets the eye.

    • Meg permalink

      Thanks for stopping by & reading, Gordon! I agree, I wish more people understood the amazing handiwork that goes into successful horticulture.

      To protect your privacy, I removed your personal contact info from your original comment. We do still have it, though, so if any info on your account needs to be updated, we’ll be sure to do that for you! :)

  7. R.H.Smith permalink

    I have planted avocado seeds for several(20+) years. Many have produced good size fruit. Many have been non-producers. I plant them along the fence row. If they produce it’s great. They just need water for the first year.

    Can you tell me about any book on grafting with well illistrated graphics to help in the proper method of grafting? Most I have seen are similar to your offering(rather limited).

    • R.H. Smith, I don’t know any book off-hand that gives the kind of detail you’re looking for on grafting. Maybe someone else reading this post or the comments knows of such a book? If I find something, I will be sure to get back to you!

      In the meantime, I might suggest checking with your library or looking to see if your area has any events going on. Some places offer grafting classes and they might provide materials as well.

    • Kris permalink

      I would suggest looking into local groups. I know when we lived in California there was the Rare Fruit Growers association that came into our high school and brought the root stock and scion and showed our students how to graft apple trees, then let them keep their tree! Great experience!

    • Peter permalink

      This link will show you the common methods of grafting, but it doesn’t really explain the idea behind grafting. To understand why grafting works, you need to know how a cell grows and reproduce, and I’d suggest starting off with learning about the meristem and vascular cambium.

      I’d recommend using your local library to look for plant propagation books, which will usually discuss grafting. For my plant propagation class, I had to use Hartmann & Kester’s Plant Propagation: Principles and Practices (8th edition), and I personally liked it, although I haven’t really read any other plant propagation textbooks so I don’t know if it’s the best out there.

    • Jack Graton permalink

      Hi, you can try: “The Grafter’s Handbook” by R.J. Garner, which I find to be clear, thorough, (I’ve found) very useful for avocado, etc. You can also get info from:
      Jack G.

  8. The Missouri Nut Growers Association will hold two grafting sessions in early May. The one near Collins MO is on the 5th and the one outside Washington MO is on the 8th of May. See for more information. Check the site after April 1 for added details.

    • Barb, how great! Those events are always so educational. Thank you for sharing this. I sent out a Tweet about it to our local Twitter followers. :)

  9. Pat permalink

    I apply epsom salt on drip line of my fruiting, or flowering trees to help them to bloom. If you buy it in garden centers it will have direction on how much to put on plants or trees. Epsom salt is a mineral I guess the trees need. I know it will cause the tress to bloom more but this year I am going to see if it will cause the trees to hold the blooms. I trimmed by meyer lemon tree back in feb. and it is full of blooms already and has small lemons on it. Just a suggestion.

    • Pat – excellent advice! I was going to mention that the lemon plant enjoys a little epsom salt application, but you beat me to it. ;)

  10. Pat permalink

    I just planted my first apple trees this week and I am anxious to see if they will do well here in the southeast Texas.
    I for to say my satsuma and orange trees are blooming like crazy also.
    I love working with plants and learning about them and I have been wanting to try the grafting but never had the nerve to. lol

    • Pat I bet Texas has some grafting events once in a while – you should attend one and tackle the grafting beast! :)

  11. Jim permalink

    Just a thought about the HoneyCrisp apple and the Goldrush as a pollinator. Maybe a better pollinator like Jonathan would be better.

  12. Stan permalink

    Nearly 30 years ago I purchased some product from Stark and have sinced moved. I had great success. We are moving into a newly built home and have started over again. I have received multiple magazines from different nurseries but think we will stick with Stark. Thanks for the years of quality.

    • Stan, than *you* for growing with us. It’s a pleasure to supply the quality product you’ve had such success with over the years. Here’s to many more! :)

  13. Leslie's Farm permalink

    I have had the same experience. In most of the places I have lived in the past 25 years, there are wonderful Stark fruit trees. I have returned to spy on some of my past plantings and even in the case of benign neglect, I saw beautiful trees – some dripping with fruit! However, when I moved to Texas I thought long and hard about finding a local supplier. After I checked out what I could find I decided to stay in my comfort zone, order from Stark and see if the trees could handle the often harsh climate of Central Texas. To add to their test their first year was the already legendary, worst drought in 50 years. I am happy to say that my little green friends from Missouri came through it like the excellent stock that they are. AMAZING! Oh, they suffered like everything did, but they seem quite normal for new transplants starting their second year. One of them, the Granny Smith, never went dormant, but I learned that mature trees of this variety often produce twice down here. And, it has been a very strange Winter.

    • Thank you for sharing your experience, Leslie. The terrible heat and drought (and fires) in Texas and Oklahoma last year devastated an unthinkable amount of the local trees, so it is touching to hear your young fruit trees survived! :)

  14. skip kemp permalink

    I noticed that the original graft on three walnut trees I recently purchased was pruned off and a side branch that budded off the original scion was allowed to become the main “trunk”. All three trees were done this way.

    What’s the purpose of pruning off the original grafted scion and allowing an axial bud to become the trunk?

    • Hi there, Skip! Are these walnut trees you got from us? I can’t really speak for another nursery’s methods but, when we graft our walnut scions onto their rootstock, that bud you are seeing is actually the scion that will become your walnut tree. The part that might appear to have been pruned off was not the original grafted scion and it won’t even be noticeable once the tree gets older. :)

  15. I have some english walnut trees that I grew from seed.I’m I going to have the same problems like growing apples from seed. Also have Black walnuts that started having nuts last year.Will they pollunate my english walnuts.All the seeds I planted were from the same tree

    • Hello Ken :) There are 2 important things to know about seedlings: They are not grafted so cross-pollination should not be an issue (grafted trees are clones of the same tree, so if you have two of the same grafted variety, they will not pollinate because it’s like having only one tree there). You won’t know for sure what type of fruit/nut will be produced, if any at all, and each seedling you planted could be completely different. There really is no telling what you will get (or when you’ll get it) until it grows.

  16. Glenn Shannon permalink

    The problem I had with Stark Bros is you put moist paper around the roots but because you don’t tie the bottom by the time I get the trees the paper is at the top of the tree and it is dead before I get a chance to plant it.

    • Thank you for letting us know how your tree arrived, Glenn! The moist paper is important in keeping bare root tree’s roots from becoming dry in shipping. I will pass along your concern. :)

  17. suzanne permalink

    I’m planning on making an esparieled apple fence. How far down can the trunk be pruned without ruining the graft? I evidently need to prune much of the top for a criss-crossed pattern.

    • suzanne permalink

      Sorry… that was “espaleired˝ (belgian) apple fence.

    • Hi Suzanne! The graft for your apple tree (the “bump” near the base of your tree) may have growth around it. Pruning this growth won’t ruin the graft and we even encourage that you prune off vegetative growth that sprouts from the graft, or below it, to ensure that the top-growth (the variety you selected for the fruit) may thrive without competition. :)

  18. WILLIAM Wolff permalink

    I bought a royalton cherry tree that did great the first year budded the second but now the top of the tree is dead but growing like crazy below the ‘graft’ should i leave it or pull it out?

    • If the tree has died above the graft, what grows from the rootstock will not be the Royalton™ Sweet Cherry you intended to grow. The rootstock is simply used for determining things like height and anchorage of the named variety so there is no telling what type of tree it will become on its own.

      I am sorry to hear your tree did not survive, William, but if you want a cherry tree that will have quality fruit and certain characteristics, the best option would be to pull out what’s left of the tree and give growing your own cherries another go. :)

  19. Helen permalink

    Hi there,

    I have an apple tree which I now realise didn’t produce fruit this year on its lush green growth due to over fertilizing with nitrogen (via compost tea). Thank you for the above posts.

    However, my real problem is… the grafting on the tree is under-performing significantly. Would you recommend harsh pruning of the bigger portion of the tree in an effort to correct the imbalance? And if so, at what time of the year?

    Many thanks

    • Hi, Helen! The compost tea might have been the culprit if it is high in Nitrogen. :) I’m not sure of the age of your apple tree (it could be not developed enough yet) but if you feel you are overfertilizing, try and see how your tree reacts without the compost tea for a bit.

      How is it that your tree’s graft is underperforming? I’m curious what this means. Pruning will definitely help create balance between the top growth and the root system, and it will also allow for a sturdier physical structure as your apple tree grows. Any heavy pruning should be done when the tree is fully dormant in the late fall/winter/early spring (before bud break) — this not only helps to avoid shock to the tree, it is easier to *see* what you’re pruning without the leaves hanging there! ;)

  20. daniel permalink

    i have a meyers lemon tree that produces very well. I grew several from the seeds this past summer and am wondering if the trees from the seeds will produce lemons or if they need to be grafted. I have been wanting to try grafting for a long time. If grafting is needed… what is a good root stock to use? I live in southeast texas,

    • Many types of citrus trees are known for seeds coming true to type, so the lemon seeds you planted may fruit and share traits of the parent Meyer lemon fruit; however, your Meyer lemon tree was more than likely grafted, and it benefits from this for 2 main reasons:

      1. The trees that grow from seed may take many, many years to mature and establish as trees before they are ready to bloom or set their first fruit crops. Grafted trees tend to produce much sooner than seedlings.

      2. The tree’s size is determined by the rootstock it is grafted to. Growing a tree from seed means the tree will try to grow to its standard height rather than being kept more manageable by a dwarfing rootstock. Also, some types of citrus trees can be susceptible to diseases in certain areas, so they are commonly grafted onto sour orange rootstocks for increased resistance.

      If you are able to find rootstocks in your area, sour orange would be a common one to use. Many varieties require that you have propagation rights before grafting etc., so you might want to do some research. If you can find a source for rootstocks, they should have more information on this matter.

  21. Patrick White permalink

    I have purchased Stark fruit and nut trees for over 30 years. Last year I left my home in Idaho where I had over 40 Stark fruit and nut trees for my new home in Alaska. My question – I would like to grow Honeycrisp apples in my high tunnel. Do you think I would be successful with a two layer permaculture approach with the rootstock used by Stark or should I try to find a rootstock which is more cold hardy. I live on the Kenai Penninsula in zone 4b. I also intend on growing North Star pie cherries in the high tunnel and three of your cold hardy peaches in containers which I will move inside for the winter.

    • Our Honeycrisp rootstock (and the tree) is cold-hardy enough for your planting scenario, Patrick! We have two suggestions though: Just to be safe, you can plant the trees a couple of inches deeper than normal. Also, opt for the semi-dwarf sized tree. Since Honeycrisp is not a vigorous grower, and is naturally smaller than other varieties, a semi-dwarf Honeycrisp tree isn’t going to get as large as other semi-dwarf apple trees would. It would remain in what we consider the “dwarf” range. The reason we suggest this is that the dwarf rootstock would probably not be ideal for your planting situation.

  22. Seth permalink

    I purchased two Intrepid peaches this past year along with a couple of apple trees from Stark Bros and have been really pleased with all of them. I have ordered a blushing star and am considering a contender for this spring. I am doing some research on winter hardiness relating to the rootstock of peaches and was wondering if you could tell me the rootstock used for your hardy variety of peaches? Thank you.

    • Hi Seth! The rootstock Stark Bro’s uses for our dwarf peach trees is Peach Redleaf (a Tennessee Natural type) and Lovell rootstock for our standard trees. Both are moderately cold hardy rootstocks. I hope this helps!

      • Seth permalink

        Thank you, Sarah for the prompt reply and information. It was -23 *F here this morning, the coldest it’s been in years, so it will certainly be a good test for my young peach trees.

  23. Huguette permalink

    I planted a new 5-in-1 apple tree last year in May. It produced a few apples in the summer.

    The problem this year is that half of the grafted branches are not growing leaves, therefore no flowers. The other half look fine with healthy looking leaves and apples forming. My question- will the unproductive branches going to grow next year or is it a lost cause?

    • If the unproductive limbs are dead, they won’t be able to flower or fruit, so I’d suggest scratching the bark on these branches to see what their status is. Greenish, wet wood beneath the scratch is living tissue. Brownish, brittle/ dry wood beneath the scratch is dead tissue.

      If they leafless branches are actually living, they may still send out growth this growing season and in future seasons.

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