Take issue from seed if fertilised (6)
I believe the answer is:
differ
'take issue' is the definition.
(I've seen this before)
'from seed if fertilised' is the wordplay.
'from' indicates a hidden word.
'DIFFER' is hidden in the letters of 'seed if fertilised'.
(Other definitions for differ that I've seen before include "Contrast - disagree" , "Disagree, take issue" , "'Disagree, dissent (6)'" , "Be dissimilar" , "Have opposing opinions - beg to . . . . . ." .)