Chocobos can be trained once per hour, and will demand one of the following fruits or vegetables as a reward for their efforts:

Krakka Root / Curiel Root / Sylkis Bud / Mimett Gourd / Tantalplant / Pahsana Fruit / Thavnairian Onion

These fruits and vegetables can be obtained through gardening.

From:
http://na.finalfantasyxiv.com/lodestone/topics/detail/3d01271ad3add3638e42b642e8ad4bb4db15ca50

I don't want to sound like a downer for a feature I've been waiting ages for but... acquired by gardening? :'3

Hoping there's an alternative to acquire these aside from gardening. Added Level 3 tier nodes even, would be nice..?

Er... sorry if I am mistaken but I don't think there's enough garden space to go around to supply a big fc's members for all their chocobos.

Some clarification would be appreciated.