One thinks of a line in chaff! (5)
I believe the answer is:
brain
'one thinks of' is the definition.
The definition suggests a singular noun which matches the answer.
'a line in chaff' is the wordplay.
'a line' becomes 'i' (I am not sure about this - if you are sure you should believe this answer much more).
'in' means one lot of letters goes inside another.
'chaff' becomes 'bran' (bran is a kind of chaff).
'i' going inside 'bran' is 'BRAIN'.
Can you help me to learn more?
(Other definitions for brain that I've seen before include "and 15 ac. The loss of experts through emigration" , "Intellectual capacity" , "It's in the skull" , "Thinking thing" , "Control centre of nervous system" .)