The most common and most likely answer to this crossword clue is the 9 letter word SUBSTRATA
I've seen this crossword clue in The Guardian
S
U
B
S
T
R
A
T
A
Buddy explains!

The straight part
We know that "Lower seams" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case lower seams = substrata.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 SUBSTRATA mean?
SUBSTRATA noun- A layer that lies underneath another.
- The underlying cause or basis of something.
- A substrate.