I associated my account with another yahoo account, and after that I lost 50 reputation. Why is it so?
Your reputation here doesn't get affected by association of your external accounts. It does get affected by your linking of your Stack Exchange network accounts. For example, I see you have >200 rep on Stack Overflow, and <100 rep here on Meta Stack Overflow. Try this:
You should be able to do the same thing on the Programmers SE beta. Please try that, and update your question if you don't get the expected behavior.