By a whisker, beat seed (3)
I believe the answer is:
pip
This clue is a double definition.
'by a whisker beat' is the first definition.
(to pip someone can mean to narrowly beat them)
'seed' is the second definition.
(I've seen this before)
(Other definitions for pip that I've seen before include "Small hard seed" , "Narrowly defeat" , "Palindromic pear seed" , "one signals lieutenant" , "Spot (on card); seed (of fruit)" .)