Have you tried to use plugin Active Directory Attr Sync? There is option to fetch and synchronize data from AD server and use it in JIRA. You can use one of post functions: change assignee to user manager or you can use post function to copy manager of user to single user custom field and use it in conditions/post-functions.
Here you can find more information about this plugin: https://intenso.atlassian.net/wiki/display/AD/Active+Directory+Attributes+Sync+Home
I hope I've helped you.
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