Instead of getting all wrapped up in analyzing the wording of each individual answer and spending a lot of time on that, the way I looked at this sentence was by understanding the overall meaning and what was being compared.
The use of "although" as the initial opening word indicates that the sentence is comparing two different ideas. The first phrase indicates the cacao plant
ORIGINATED IN the
UPPER AMAZON REGION, and the second phrase says its (refers to the cacao plant) first cultivation for seeds and pulp was apparently
BEGUN IN MEXICO AND CENTRAL AMERICA. Comparing these two different verbs and places, I can already clearly see that the use of "begun in" is incorrect since begun, beginning, etc. is a verb used to describe TIME not a PLACE whereas the use of "originating in" is clearly used to describe a PLACE, the Upper Amazon region.
Therefore A, B, and E can all be immediately eliminated since all use variations of begun, beginning. D can also be eliminated since "to be" is incorrect since it is nonsensical for "the beginning of its cultivation for seeds and pulp TO BE in Mexico and Central America". Beginning of something, which indicates time, can't "be" in a place. Beginning of something begins in a time.
C then clearly is the only choice that stands out to fit in the comparison of the sentence, and when plugged into the stimulus clearly compares correctly.
Although the cacao plant probably originated in the upper Amazon region, it was apparently first cultivated for its seeds and pulp in Mexico and Central America.