Stain part of flower (6)
I believe the answer is:
stigma
I believe this clue is a triple definition!
'stain' is the first definition.
(I know that stain can be written as stigma)
'part' is the second definition.
(stigma is a kind of part)
'of' acts as a link.
'flower' is the third definition.
(thesaurus)
(Other definitions for stigma that I've seen before include "part of plant" , "Disgraceful mark" , "Sign of disgrace" , "Part of a flower" , "Mark of infamy or disgrace" .)