Yes, you can!
In the configuration of the User Directory, you can specify group filters. Only the groups that pass this filter, will be synced with Jira.
To create such a filter, you can create a default LDAP query. To get you started, you can look over here: http://confluence.atlassian.com/display/CROWD/Using+Apache+Directory+Studio+for+LDAP+Configuration
If the question is still valid nowadays, feel free to ask for more indepth instructions!
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