The most common and most likely answer to this crossword clue is the 9 letter word PHENOTYPE
I've seen this crossword clue in The Times
P
H
E
N
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T
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P
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Buddy explains!

The straight part
We know that "Make-up" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case make-up = phenotype.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does PHENOTYPE mean?
PHENOTYPE noun- The appearance of an organism based on a multifactorial combination of genetic traits and environmental factors, especially used in pedigrees.
- Any observable characteristic of an organism, such as its morphological, developmental, biochemical or physiological properties, or its behavior.
- To evaluate or classify based on phenotype