There are numerous project management applications in the marketplace and the hiring manager is trying to find out whether you are competent using at least one.
Try to demonstrate an awareness of the alternative applications, and an eagerness to learn how to use it, if necessary.
A good answer could be:
I am very familiar with Microsoft Project and its advanced features. I understand that in the software development industry JIRA is preferred because it combines project management with bug tracking; and there is also a movement towards BASECAMP because it allows the teams to collaborate.
I am open to undergo further training to learn an alternative project management application and I am confident that my experience in Microsoft Project will help me to pick it up quickly