Well, I guess the first thing to do would be to make an event item (or not) called seed.
1. Planting
I can imagine the planting in two pretty simple ways.
A. The first is to have the seed item be unuseable and have the planting handled through an event. For instance, this could mean that in areas where it is permissible to plant, you can put an event - when the hero presses enter, it will check if he has the item seed through a conditional branch, and it will then either say "You do not have any seeds" if the condition is failed or something like: "Would you like to plant a seed here?" if the condition succeeds. This, I believe, is the simplest way. However, if you want more freedom in where to plant the seed, then the next way might be best. With both ways, however, I would not suggest being able to plant more than 10 seeds in any given map. Well, that depends, I suppose. In any case, if this is the method you want, advance to 2.
B. Have the seed item be useable, and have it call a common event. In this common event, you would first need to check if the map is appropriate. You don't want to plant things in a cave. You then need to check if the X and Y positions are appropriate. You don't want to plant things on a tree. You will then need to set special events that have IDs common to all maps in which you can plant things. This is not very simple. I would suggest against this method. If you want more details, however, I can certainly go on.
2. Watering
When you have your special planting events set up (by either methods 1.A or 1.B), you should have a second page to them that is turned on when you plant your seeds. In this, you should check if the player has a watering can or whatever, and then give the option to water them. If you water them then that should be OK. You can then set a type of loop that disallows you from watering it for however long you want using wait frames. After several waterings, you can have it grow up.
3. Harvesting
Once it is grown up, it is a simple matter to harvest. Merely add another event page, and when the hero presses enter, have it give the option to harvest. If he chooses yes, then you can add the harvested item and then turn off all the related switches so that it reverts back to its initial setup.