Sometimes more than one preposition can be used, and the meaning stays pretty much the same. For example:
This happened in the year 1893.
This happened during the year 1893.
Other times, only one preposition is idiomatic. In this case, rooted in is an expression that even gets its own entry in the Merriam-Webster dictionary:
rooted in (idiom) formed, made, or developed by using (something) as a basis
Her opinions are deeply rooted in her faith.
a dance rooted in African tradition
Sometimes there is a logical reason behind the correct preposition choice. As was said in a comment, in this case, plant roots go down into the soil, so in would make more sense than on or at. But I can see where it might be confusing, especially because of the way we say based on this, but rooted in that.