Apple Tree Issues

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So one of my apple trees is getting worked over by something. My tried and true remedy up till now has been neem oil, but not only is it not working on aphids this year, but it's not helping the one apple tree either. See attached pics.
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Your apple tree is weak and diseased from root damage. Can you post a photo of the tree trunk going into the ground?
 
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Oh wow, if that's the case, how to fix this?
 

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I don't think your tree is going to ever be healthy again due to the tree's conditions now.
 
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What of the new growth coming up from the trunk? Should I trim off the bare branches and allow this growth to grow as apposed to the normal pruning them?
 
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And how did the tree get to this state? I've got three other apple trees and sure as heck don't want them ending up like this.
 
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Looks like it's planted too deep in the ground and the wrong location. When you buy expensive fruit trees, it's best to have your soil sample sent to the lab for a soil analysis. Most local Universities will test soil and give recommendations. All soil tests will make recommendations if you ask, whether or not the trees are suitable for the soil tested. A test will run you about $30 and is worth every penny.

Also when trees, shrubs, ornamental plant, or even lawns starts to show disease. The owner should have a soil analysis to find out if it's the soil that's the problem. Sometimes the problem is from excess macronutrients and the only way to find out is with a soil analysis. You can save a lot of time and effort with a soil test. Its all just a guess without an analysis.
 
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Good to know. What you're saying though is this tree can't be saved? It does have new shoots coming up from the trunk.
 
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If you bought a grafted tree and allow the shoots to grow you may get the bottom cut instead of the top of both trees.
 
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Ok, so from what I gathered from the article, if I read correctly, is that the shoots coming up may actually be a different kind of apple because they come from the root and not the graft? I'm ok with this. Would I need to cut off the remaining branches and just let it grow?
 
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The main issue is that the root stock is selected not for it's apples but for it's ability to grow well in the climate it's being grown in. Looking at those pics I don't even see a bulge indicating a graft so it may have been buried. Thing is, without knowing what your root stock is you're likely wasting your time but hey if you want to try it go for it.
 

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