Last year, I planted brown cotton from seeds I had ordered. That's one of the bolls in the photo. The yarn spun up to a lovely color just like the cottonboll. I also spun up some brown cotton I had bought somewhere along the line but most of it was my cotton. After spinning and plying, I boiled the cotton for about 45 minutes. As you can see, most of it is no longer brown but a really nice shade of green. I love the way it turned out, but wish to know how this happened. I've planted green cotton this year and the seeds look nothing like the brown seeds I planted last year of brown cotton.
The skein on the right is from white cotton I grew 2 years ago plus a little purchased cotton thrown in.
Both are really, really nice, but I'm tired of spinning cotton and have moved on to wool for awhile. After spinning the cotton, the wools practically spins itself.
postscript: The following is an explination I got from a friend in the know.
The reason your brown cottons and green cottons look different is because they are different genetic strains. There are also cottons that look brown, for instance, but the other gene in there is green. so when it breeds, it will not breed "true" and may result in a green cotton.
Modern white cotton has been bred very seriously for hundreds of years and the colored natural cottons were raised in a much more primitive farming approach in Peru, etc. so while they maintained the colors, they may not have bred for staple length or a certain kind of color.
If you garden, you may notice the squash phenomenon here. If you have volunteer squash or seeds from squash you have grown, there is also a chance that they will not breed true, or will create squashes you hadn't expected...this is a very similiar issue!