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I rooted a fig cutting back in the spring and now have a 2 foot baby tree with a single leader and no branches. Do I prune the leader during the winter or will the tree branch out on its own next spring?

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Leave as is for now until spring. Likely it would send out lateral buds in the spring, but you can without fear cut off the top half, cut this piece into two six inch sections so one of them will have the terminal bud and root both of those, the remaining rooted section may take a little while to send out buds but keep the roots moist but not wet and all should be well. From the cut end of the already rooted piece you could expect two side shoots to emerge giving a Y shape to the new plant. Of the two new pieces, one will have a single leader from the terminal bud and the other a Y shape once they all get going.

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<based on nothing just imagination> I would leave the tree alone until it has outgrown the "will it survive this winter?" age. And only after that start aggressively trimming following all the rules of thumb of course. I would imagine that is when 2-3 years have passed and the plant is as tall as You.

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