These areas on the trunk are referred to as burr knots. They are a form of adventitious root growth. "Adventitious" means root tissue growing from plant tissue that doesn't normally develop roots. This sometimes occurs on fruit trees that are grafted (which apples typically are). Over time, these may lead to structural weaknesses in the tree or an entry point for insect pests. That said, our entomologist who grows fruit trees has the same type of adventitious roots on some apple trees and they still continue to be productive and bear normal fruit. 

There is nothing you need to do. We do not recommend using any type of wound sealant or any type of treatment for this. Since it is a young tree, make sure to keep up with watering during periods of drought and make sure your mulch layer is not too deep (no more than 3"deep and avoid putting mulch directly against the trunk).
https://extension.umd.edu/hgic/topics/watering-trees-and-shrubs
https://extension.umd.edu/hgic/topics/mulch

Here is our page about apple tree care in general. Note that pruning and following a spray schedule is recommended for good fruit production.
https://extension.umd.edu/hgic/topics/apples 

Christa

Thanks very much for your answer, Christa.

My apple tree is indeed a grafted tree. In fact, it has 4 different types of apples in a single tree. 
I planted it in the spring of 2017, but I think it was probably 2-4 years old when I bought it from Home Depot.
So these burr knots will not get worse? I will leave the tree alone as you suggested, but it seems to me these burr knots are really weakening the tree.

Thanks again.

Hi- if your tree is experiencing poor growth, the cause is not the burr knots. Possible causes include compacted soil, inadequate space or sunlight, too much or too little water, weather extremes, and insect pest and disease issues.

We recommend that people not plant apple trees with multiple grafted cultivars because the different cultivars have different branching and fruiting habits, and environmental and nutritional requirements. This makes caring for the tree and encouraging good fruit production quite challenging. 
Jon

OK, thank you Jon.