Deficiency in desert (6)
I believe the answer is:
defect
This clue is a double definition.
'deficiency' is the first definition.
(I've seen this before)
'desert' is the second definition.
('defect' can be a synonym of 'desert')
'in' acts as a link.
(Other definitions for defect that I've seen before include "Imperfection - go over to the enemy" , "Desert - fault" , "Leave the country" , "Fault - default" , "'Flaw, imperfection (6)'" .)