First thing I notice:
4367.29 ms - 95073 rows - 2 columns
Your qa_options table has over 95,000 rows! Q2A core has around 300 options, most plugins only add a handful of options.
So you must have a plugin that's added thousands of options somehow. You should check through your table and see where they have come from.
Most likely it's a bug with a plugin that keeps adding options with different names.
Or maybe it's from a bunch of plugins you have installed at one time but then removed. Over time, adding and removing plugins leaves options in the table that are no longer used.
Edit: if you're not sure which options are filling up the table, try this query in phpMyAdmin:
SELECT SUBSTRING(title, 1, LOCATE('_', title)) AS sub, count(*) AS num
FROM qa_options GROUP BY sub ORDER BY num DESC
That will show you which prefixes for options are most common, e.g.