A looks good to me so I'll take a look at the other options and try to eliminate. If I find something better than A than I'll go with that instead.
B - The phrasing 'from when agriculture began' is very awkward and its placement next to 10000 years (which shows duration and not a specific time) is also wrong. A is better.
C - The phrase that which had been is very awkward. It also breaks the 'which' rule. A is definitely better
D - 'It' refers back to the same growth which is incorrect. The two growths are different. Also the phrase 'from when agriculture began' is a problem as in B. A still wins
E - 'It' is a problem as in D. The 'did' is also a problem because the growth did not do anything for the 10000 years; it 'has been' something for these years.
Thus A is the winner.
This was a difficult question because I couldn't really do a split on this, so on tough questions it might be a good idea to select one option that you like the most and evaluate the others against this.
(Answer from Aristotle Prep)