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Unlike the mushrooms we eat most of the time, which grow above the ground, truffles grow underground in natural woodland.

'Which' in this sentence refers to 'the mushrooms' and it is a relative pronoun.

I often see such pronouns stand right behind the noun they refer to. For example: The man who is sitting is my friend.

But in the first sentence, 'which' is not in its usual position. Could you give me an explanation for it?

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Nhật BìnhBut in the first sentence, 'which' is not in its usual position. Could you give me an explanation for it?

While it is less common, it is not wrong to place a few words between an antecedent and the relative word that refers back to it.

I'm working on a big book right now, which I hope will be published next spring.
The closest residence is a home still under construction, which was not damaged.
Are you acquainted with the passages in Huckleberry Finn which are held to be objectionable?
Williams had an MRI exam on his ailing knee on Monday, which came back negative.
Stir a few drops of red food coloring into white icing, which will turn it pink.

CJ

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Nhật BìnhBut in the first sentence, 'which' is not in its usual position. Could you give me an explanation for it?

The sentence is not as well-written as possible, but it is grammatical.

Here are a couple of alternatives.

Unlike the mushrooms we eat most of the time and grow above the ground, truffles grow underground in natural woodland.

Unlike the edible mushrooms that grow above the ground, truffles grow underground in natural woodland.
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Nhật BìnhI often see such pronouns stand right behind the noun they refer to.

There's no rule that says that has to happen.

Both forms are common.

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