Placing kernels in water on Shabbos:
One who soaks wheat or barley and the like in water in order for it to grow is liable for the planting prohibition. This applies even if one soaks only a single kernel. For this reason it is forbidden to place kernels in water with intent to leave them there for enough time for them to be able to grow. However it is permitted to place the kernels there for a short amount of time, such as to place barley within water for animals [which one owns] for them to eat right away.
May one remove kernels that have begun to grow from within their water?
No. One who does so is liable for the uprooting prohibition.
May one remove an avocado pit from water if it has begun to sprout?
May one plant seeds in the ground on Shabbos with intent to remove them prior to growing?
 Doing so is a secondary prohibition under the planting Melacha. [ibid] Regarding if one is liable immediately upon entering the seed into the water, or only later on when it grows. The Magen Avraham 336/12 learns one is only liable when it begins to grow, which is approximately after a half a day. So is the implication of Admur ibid. However there are Poskim which learn that one is liable immediately
 Literally “For a long time” [Admur] Ketzos Hashulchan 142 footnote 14 explains this to mean for enough time for it to grow. The Magen Avraham however writes that it refers to a half a day.
 As otherwise it is forbidden to feed animals on Shabbos.
 Now even if some kernels will remain left over in the water, nevertheless one may place tem there as it is not inevitable that these kernels will grow, as perhaps the animals will eat them beforehand. [ibid]
 Ketzos Hashulchan 142 footnote 14
 SSH”K 26 Footnote 9 in name of Rav SZ”A.
 Minchas Chinuch Mitzvah 298 p. 112
 As the liability is on the act of planting irrelevant of the results. [ibid] However see Admur 336/10 and 17 which implies that we go after the final growth and not after the beginning action.