Here are the specs for the bike: http://www.trekbikes.com/us/en/bikes/2009/archive/23
But it doesn't specify the chain.

As a guess, I'd say the chain is Shimano 105, since all components are 105 except for the Ultegra rear derailleur.

I bought a Madone in 2008 and all was Ultegra except the chain was 105. And the chain had a master link in it.