Although farmers have a number of ways to raise young fish, most are grown in earthen ponds. separates items in a series separates coordinate adjectives (adjectives that independently modify the same noun) joins two main clauses sets off an introductory clause, phrase, or word sets off a nonrestrictive modifier (modifying words that could be removed without loss of meaning)

The use of the comma in this sentence is to set off an introductory clause, phrase, or word.

There is no list of items in this sentence. There are also no coordinating adjectives. 

Furthermore, the comma does not separate two main clauses. We can tell this because "Although farmers have a number of ways to raise young fish" cannot function on its own as a sentence.

Finally, "Although farmers have a number of ways to raise young fish" cannot be removed without loss of meaning. It's important for the reader to know that there are a number of ways to raise young fish. That means the final option (a nonrestrictive modifier) is not correct.

Therefore, the best answer is the comma is used to set off an introductory clause, phrase, or word. The word "Although" is another clue that this is the right answer.