Helping Vitae out of the well at the beginning of your adventure also releases the multitude of Harvest Wisps throughout the world. As nobody knows how to grow crops anymore, you won't find any seeds for sale in the stores. Instead, these little fairies hold the seeds you need to use to introduce farming back to the towns.
Harvest Wisps will appear throughout the world as little floating blue dots. Simply walk up to the wisp and interact with it to receive 3 bags of seeds, after which the wisp will disappear. Not to worry though; it will return to that exact spot soon enough! Some wisps reappear every day at the same time of day without fail, while others are a bit more random as to when they want to show up.
(If you are only getting 1 bag of seeds per Harvest wisp, update your game to ensure you have the 1.5 version patch that changed the wisp handouts from 1 bag to 3 bags.)
As you grow and help the worlds' towns with the knowledge of farming, you'll also unlock more Harvest Wisps because the Harvest Goddess' power is slowly growing thanks to your efforts. You'll soon find all sorts of new crop and flower mutations to grow using the wisps' seeds.
Harvest Wisp List
As there are no seeds at the stores, knowing when a particular Harvest Wisp is active is important as you're trying to ship enough crops to expand shop inventories. The DocPad you receive from Doc Jr will include a wisp-tracker within its world map, called the Harvest Wisp List.
Using the HWL is done by opening up the world map and pressing the appropriate button to launch the search. You'll be given the option to select up to 3 plants to target. The crops and flowers to choose from in the list are ones that you've located already, either from a Harvest Wisp or grown on your farms. Then just confirm your selection and let the HWL do its thing.
The HWL will then display icons of the plants your looking for if there are any wisps that are currently active anywhere in the world. For example, the above picture shows where we can find Corn, Wheat, and Pineapple at the time the image was saved. The crop/flower icons will disappear when the wisp is gone, and reappear when the wisp is accessible again.
The icons on the map will indicate the general area where the wisp can be found. You can see on the map that there are visual divisions between each area. So if you see an icon around Lebkuchen, you know its somewhere in that area and not farther north into Salmiakki. The issue is that it could be anywhere in the area, and most of the areas are HUGE, especially the combined Halo Halo + wilderness area. If the wisp you're searching for has its HWL icon in Halo Halo, the wisp could be in the south area of Halo Halo beach, in the coffee tree grove, perhaps by the entrance to the Pastilla desert, somewhere on the path leading to the wilderness farm or Harvest Goddess Spring, maybe by the mine or the Wedding Pavilion, or even along the road to Calisson.
It is up to you to trod through the world, checking the paths and crevasses to claim the wisps' treasured seeds. When you get close to a wisp that's tagged in the HWL, the mini-map in the lower right corner will display a green wisp icon. The icon shows up once there's enough room on the map for it to fully appear.
Not every plant in the game has an associated Harvest Wisp. Many mutations don't have wisps and can only be found by growing the parent seed in the appropriate environment and season.