stem problem

plant is only a few weeks old, and not very big. was outside, until a few days ago. when i transplanted it to a pot, i noticed that the bottom of the stem is kind of crusty lookin and skinnier, looks almost like it is dead where it goes in the dirt. but the plant looks healthy. whats it from and can i fix it? i put more dirt around the bottom right to the very bottom leaves, and it covers it up, but not sure it that will actually solve the problem. let me know if u need pics.

The very bottom of the stem, like maybe a couple of inches above the soil by harvest time, will not be smooth like the rest of the stem. It will look more like a tree. A picture will probably tell the story and we like pictures. VV