I found a thread that very similarly describes the problems I'm having with my Kumquat tree: http://www.botanicalgarden.ubc.ca/forums/showthread.php?t=27302 I got my tree several months ago and it was doing well until it came down with a case of spider mites. Thankfully, I got a spray and have eradicated them, but only after they had done damage on the existing leaves. Afterward, I was so encouraged by the sight of new growth, I didn't realize it was shooters from the root stock in the Trifoliate form. Guess I figured it would grow out of this odd leaf formation once these new shoots were more mature. So now I'm worried because I've got a couple rapidly growing rootstock shoots, but no new growth on the graft, which still has the leaves damaged by the spider mites. Should I prune off all of the rootstock shoots? I'm worried because the leaves of the graft have progressively fallen off with time, and I'm worried I'll be left with a tree with few leaves. Alternatively, is there any way I could try to graft a new Kumquat shoot into whatever this rootstock is? I don't know where I would get a branch to graft in, but the rootstock shoots seem to be very healthy and doing well.
The growth from the rootstock should be removed. Though, as you suggested, the shoots could be pruned so as to leave short stubs to allow for grafting of more desirable varieties. The problem of the scion dropping leaves should be addressed. What condition are the leaves in when they drop? Are they young, healthy looking or are they old and yellowing? How many have been shed? At what rate are they being shed? What is the tree's current cultural conditions in terms of lighting, temperature, moisture, humidity, etc.?
The dropped leaves are still pretty normal looking when they fall. It's been a very gradual process, over the course of several months. So far only the original leaves have fallen, nothing from the small new growth on the grafted branch. The tree's cultural conditions are as follows: approx 3 gal. pot with citrus soil, held indoor under bright florescent lighting for 15+ hrs a day. Humidity is not great, but probably better than it was in say December/January, we do try to run a small portable humidifier in the adjacent bedroom, but its a small humidifier in a large space. Ultimately I'm hoping to move this tree outside for the summer. Again, the Trifoliate part of the tree appears to be quite healthy. The Kumquat graft hasn't had any new growth since the spider mites attacked, though its looked like it was ready to sprout new leaves several times, with each time, the Trifoliate beating it to sprout first. I'm kinda curious about the prospect of grafting onto the Trifoliate. I've found a lot of articles online that show you how to do this, but haven't found Kumquat budstick for sale anywhere. I've seen a lot of online posts about people trying to grow Kumquat seedlings from seeds, would this be a route to try? Everything I've read says its not good to grow Kumquats trees from seeds, but would seeds make a decent budstick to graft onto the Trifoliate?
At this point, it sounds like the main reason for the decline of the kumquat scion is due to the vigorous growth of the rootstock shoots. The plant's energy is being channeled to them instead of to the kumquat. The decline will continue unless you remove them. If the shoots are pencil-sized in diameter near the bottom then they could be pruned back to short stubs to allow for grafting at a later time. You may want to post an inquiry on budsticks at Citrus Growers Forum. I would not go the route of seedlings for grafting purposes; the seedling has to undergo a maturation process and grafting will not reduce the that time. It will be a number of years before it will begin to bloom. I mentioned humidity earlier as, in my experience, the kumquat seems particularly sensitive to lower levels. I kept losing plants until I raised the humidity.