Github has a way of linking issues with commits. You just mention the issue in the commit e.g. 'This commit closes #1' and i believe the issue will close with that as well, but it will show up in the issue.

Jira and other ticketing systems can often read repos and look for ticket ids. In my commits at work I just mention PRJCTNAME-142 and that'll link to a ticket and aggregate in jira all the commits/pull requeusts/branches... tagged with that

Our internal system has some integration between Jira and Github, such that if you comment a commit with the ticket number then you can see them all in the Jira ticket.

RTC works like that. You can also set up rules so that you can't even check in without linking a ticket.