Those sorts of niche situations are difficult. If it is an NPC, then you maybe don't need to worry about it.
If it is a PC (especially a Pure Mortal) my choice would be to take 1-3 ranks of Performance, Scholarship or Craftsmanship, then add a few Stunts which give bonuses specifically to Gardening.
The primary gardening skill would depend on the character concept:
Performance would mean the character would be able to express himself artistically in other ways besides gardening, but not as well. This character would be focusing on having a good eye for color, impact, scent.
Craftsmanship would mean that the character is mechanically inclined, which could allow him to make minor Declarations about mechanical things even outside gardening. Maybe his gardening relies heavily on irrigation technology.
Scholarship would imply that the character is well-read and/or knowledgeable about a variety of things. A research gardener. May know other biological or general science trivia.
And if you take multiple of these skills, you can make a variety of effective declarations to really add punch to the gardening efforts. Like:
"Every Last Drop" (Craftsmanship), "How Green Does Your Garden Grow?" (Scholarship), "Breathtaking Arrangement" (Performance), "Experimental Fertilizer" (Scholarship), "The Nose Knows" (Performance), "Look at That Terracing" (Craftsmanship).
Then use Stunts to customize it. Look at all the trappings of other skills you would want this character to be able to replicate using gardening. Maybe a stunt giving a +2 bonus to Gardening-related skill checks using that primary skill, and another to give a bonus to how quickly those checks take. Think of a few other possible applications and then make Stunts for those Trappings. Or maybe Stunts to move other skill trappings to whichever skill you choose for gardening. Like First Impressions: get a bonus if you are able to leverage your horticultural acumen to make a First Impression. Or move some Empathy trappings over: "Hard day? Here, smell this flower... it is said to soothe the worst moods."