A rootstock is linked to indicator of alternative source of roughage (5)
I believe the answer is:
orris
'a rootstock' is the definition.
(preparation of iris rootstock)
'is linked to indicator of alternative source of roughage' is the wordplay.
'linked to' says to put letters next to each other.
'indicator of alternative' becomes 'or'.
'source of' indicates taking the first letters.
The initial letter of 'roughage' is 'r'.
'or'+'r'='orr'
'is' put after 'orr' is 'ORRIS'.
(Other definitions for orris that I've seen before include "Type of flower" , "Iris root in perfumery" , "Fragrant rootstock" , "Flag" , "Fragrant iris extract" .)