Answer: You can leave the young branches alone, but eventually they will become large and thick. Pruning large branches is harder than pruning small ones, and it's harder on the plant, too, because of the larger wounds they will create. Wait until the tree is dormant and prune the lowest branches off so the tree can develop a tree-like canopy instead of looking like a shrub.
Some Pecan trees require a second tree for pollination so you may have to do some research to find a suitable companion for your sapling. Carya illinoensis can take from 10-20 years before it will bear its first crop of nuts.
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