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...but I dont think he will be happy about my leaving the company to pursue full-time graduate studies.
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My guess is that is exactly why they prefer a letter from your current supervisor. An applicant who requests a recommendation from their current supervisor is showing a very strong commitment and is less likely to be talked out of going to grad school by one's boss or family after getting an acceptance letter, especially considering the cost of an MBA program and the fact that there are competing online and weekend MBA programs that allow one to earn an MBA while continuing to work, e.g.
MBA Online / MS Online through Indiana University and
University of Florida MBA Programs.
BTW, for more info about online MBA degrees:
The best MBA degree - Distance Learning Discussion Forums
site:degreeinfo.com mba
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If I do not have my current supervisor as a recommender, how do you think it would affect my application?
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I would ask that MBA program and also ask about their admission statistics. To avoid them just stating the obvious ("it depends on your overall application"), it may help to ask:
1. what percentage of applicants were accepted
2. roughly how many accepted applicants had the recommendation of their current supervisor
There is usually nothing to lose by asking such questions since the people who answer them are typically not on the admissions committee.