So rot affected the trunk (5)
I believe the answer is:
torso
'the trunk' is the definition.
('torso' can be a synonym of 'trunk')
'so rot affected' is the wordplay.
'affected' indicates an anagram.
'so'+'rot'='sorot'
'sorot' with letters rearranged gives 'TORSO'.
(Other definitions for torso that I've seen before include "Body without head, neck and limbs" , "Trunk of human body" , "part of body will be found" , "Roots out in trunk of the body" , "Body's trunk" .)