It is hard to tell for sure from your photo, but it looks like the lower branches are actually coming from the rootstock (if that swollen area is the graft union). If that is the case, you definitely want to remove them since they won't be the nectarine you are expecting. They are also robbing some of the energy/growth from the rest of the tree.

It looks to me like a genetic dwarf with a large rootstock sucker coming up in the middle. Does the short growth at the bottom have it's buds really close together? If so its a genetic dwarf.I'm looking at it on my phone so I may be wrong.

Never mind I looked at it on my pc and I was wrong. Sorry guys

I would get rid of anything lower then 24" (other then main) then pick 3 low branches to fan out, and get rid of the rest including the main. then make sure the three grow out at 45 degrees, you can tie them down if needed. This is a common method on peaches, so you can read more on that.

It's very hard to tell because there is too much shading in the picture, which makes me believe that you've planted the tree in a spot that receives too much shade.
That's why the tree has produced a dominant leader at the sacrifice of very short laterals. Nectarines should be grown on an open vase system, so that the sunlight can penetrate to all of the fruit. If this is truly the case, I'd move the tree to a much more sunny spot, and prune it back to an open vase system.

Some interesting posts here....Anyway, like Z says: make sure your saved branches are above the graft (very important). It looks like to me those lower two branches might be right at the graft. If that tree is in the shade in January...that is no problem. A sunny Spring/Summer is what you need. Keep in mind that peaches/nectarines always bear fruit on last year's wood. Find out exactly what variety this is...and figure out the expected height. It looks like it is getting pretty "leggy".

Lower branches are definitely coming from rootstock or so close to the graft union they should be removed (red lines). I too generally recommend preventing branches lower than 24" from the ground as it interferes with mowers.

Since it is winter time and the shadows are long I don't know how others can evaluate sun exposure during the growing season. I see it was taken at 9AM yesterday morning = southern exposure.

I'd likely do nothing more THIS SEASON and let the remainder continue growing since removing those lower branches will come close to removing 1/3rd of the upper tree mass. I might remove clusters so a single branch remained that was either oriented in the direction I wanted or the thickest (vigorous) one. I do like the branch angles they appear to be taking. You could also head it back (OPTIONAL! yellow line) above the middle branching to try and stimulate branching to produce an open vase form if that is what you want. There appear to be several decent branches in that area that are likely oriented radially looking down upon the tree in a 120 or 90 degree from one another at a reasonable height. I am not a big fan of cutting good tissue but it is your tree and your choice of what you want. When in doubt leave it...it can be removed the following year, but once cut cannot be put back.

kudos to someone on this forum today for providing me with the below link....

Here is a link that might be useful: Training and Pruning Your Home Orchard

This post was edited by Fascist_Nation on Sat, Jan 3, 15 at 14:57

this tree guy.. doesnt see the root flare ...

could you poke around the soil .... at the trunk ... and find out.. how deep the first root is???

tree trunks are made to be in the wind.. they prefer to be dry ... if planted too deep ... and the trunk stays constantly damp ... trouble can start ...

pruning NEVER killed anything.. so get it out of your mind.. that by cutting off some pieces.. its going to die ...

fruit trees are grafted ... the part below.. is a plant that is useless as a fruit tree.. but aggressive in root growth .... as noted above ... we do not want any useless branches .. from the root part ... they have the potential.. to suck the life out of the good part... now that is drama ... lol ... with a better pic of that area.. these fruit nuts.. can clearly tell you.. which to cut off ...

and the only trick to cutting them off.. is to leave no stubs .... google BRANCH COLLAR ... to see a proper cut ..

good luck

ken

Here is a link that might be useful: i did it for you ...

The tree looks as though it is already completely spurred up and ready to fruit without adequate vigor. This can be an issue with nectarines as they tend to be much less vigorous than peaches.

Obviously, at its present site, mowing is not an issue and those lower limbs may be your most vigorous wood, so you don't necessarily need to cut them if they are above the graft union.

If it was my tree I would top it as suggested or all the way down, just above the highest of those lowest branches, and start the open center right where the tree is trying to- if those branches are connected to scion wood (above the graft).

The spur action is not helpful at this stage and you at least need to remove the flowers as soon as they show themselves. I would probably stub them back even before this- I mean, if you save that part of the tree.

Make sure tree has adequate nitrogen and water this spring. You need to get it going. Peaches and nectarines should produce strong annual wood- at first to develop the scaffolds and then to produce fruit. 12-24" shoots are the minimum for a young healthy tree.