1 a : to cut into or sever usually by repeated blows of a sharp instrument b : to cut into pieces — often used with up <chop up an onion> c : to weed and thin out (young cotton)
[M-W's Col. Dic.]

Why would you thin out young cotton?
I can't say I've ever heard this specific use but it seems fairly logical. You would do this to get rid of the competing weeds and stop the cotton plants getting too congested, so that the remaining plants have a better chance of growing big and strong.
Thank you.