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Boris Johnson's former ethics adviser Lord Geidt says he quit after being placed in an “impossible and odious” position over a plan to risk breaking the ministerial code.
In his resignation letter, he said it would "make a mockery" of the rules, adding "I can have no part in this".
He told the PM he had considered resigning over Partygate.
But it was a request for advice on a trade issue that had left him with no choice but to quit.
Replying to the letter, Mr Johnson thanked Lord Geidt for his service but said he was surprised by his decision to resign.
The prime minister said he had sought Lord Geidt's advice about a potential future decision related to the Trade Remedies Authorities.
He said he wanted to seek advice on "protecting a crucial industry, which is protected in other European countries and would suffer material harm if we do not continue to apply such tariffs".
He added the proposal would be in line with "domestic law but might be seen to conflict with our obligations under the WTO [World Trade Organisation].
By seeking Lord Geidt's advice, Mr Johnson said he wanted to "ensure that we acted properly".