More specifically, "Alma Mater" refers to a person's college or university where one is generally an alumni or otherwise very proud of said school. According to Google, the BCS is a college football tournament, established 1998. Additionally, Wikipedia tells me that only 11 teams have ever won. Therefore, we can conclude that Meghan McCarthy, a writer of several My Little Pony: Friendship Is Magic episodes, went to one of the following colleges:
Florida State University
University of Oklahoma
University of Alabama
Louisiana State University
Ohio State University
University of Florida
Auburn University
University of Miami
University of Texas at Austin
University of Southern California
University of Tennessee
Free Cake, out.

Alma Mater is Latin which translates into "Fostering Mother". Although I couldn't tell you what the BCS Championship is.