Bother to put on duck sauce (5)
I believe the answer is:
Here is my best explanation:
'sauce' is the definition.
'bother to put on duck' is the subsidiary indication.
'bother' becomes 'pest'.
'to put on' is a charade indicator (letters next to each other).
'duck' becomes 'o'.
(Other definitions for pesto that I've seen before include "Basil and pine nuts sauce", "Italian sauce containing basil", "sauce involving Basil", "Basil and pine nut sauce", "Pasta sauce variety", "Pasta sauce based on basil", "The sauce", "A sauce served with pasta", "Basic sauce" and "It. basil sauce".)