It follows the government's decision to scrap key climate targets and its response to a review into gender services.
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Harvie, Yousaf and Slater
The SNP's power-sharing deal with the Scottish Green Party has been scrapped.
Scottish Greens co-leaders Lorna Slater and Patrick Harvie were seen walking out of Bute House before an emergency cabinet meeting. The Greens said the SNP had 'sold out future generations'.
It follows the government's decision to scrap key climate targets and a pause on the prescription of puberty blockers for under-18s.
The SNP will now form a minority government.
First Minister Humza Yousaf said he had formally notified Ms Slater and Mr Harvie that the agreement - which was signed by the two parties following the Holyrood election in 2021 - had been terminated.
The deal saw Mr Harvie and Ms Slater given junior ministerial roles within the Scottish government in return for Green support for the government's policies. Both will now leave their posts.
Of Scotland's 129 parliamentary seats, the SNP hold 63 while the Greens have seven. The Scottish Conservatives hold 31 and Labour have 22.
Humza Yousaf faces a vote of no-confidence next week with the Scottish Greens planning to vote against him
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Humza Yousaf is considering his next moves after ending the power-sharing agreement with the Scottish Greens.
Yousaf cancelled a speech he was due to give at Strathclyde University on independence but will make another speech in Dundee later.
The BBC understands he will not be announcing his resignation.
Scottish Labour says it will table a motion of no-confidence in the Scottish government later on Friday.
The Scottish Conservatives have already drawn up a no-confidence motion in the first minister, which is different from the Labour motion, which could be voted on next week.
On Thursday the Greens said they would vote against Yousaf, meaning his survival may depend on the vote of the sole Alba MSP Ash Regan.
Mr Yousaf had been facing two votes of no confidence later this week that he was not certain to win.
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Humza Yousaf is to stand down Scotland's first minister once a successor is found.
He said he had made the decision after spending the weekend reflecting on what was best for the SNP, the government and the country.
Mr Yousaf said he had concluded that someone else would need to take over in order to 'repair our relationship across the political divide'.
Speaking at his official Bute House residence in Edinburgh, Mr Yousaf admitted that he had 'clearly underestimated' the hurt he had caused the Greens by ending the agreement in the manner that he did.
He said: "After spending the weekend reflecting on what is best for my party, for the government and for the country I lead, I've concluded that repairing our relationship across the political divide can only be done with someone else at the helm. I have therefore informed the SNP's national secretary of my intention to stand down as party leader."
His resignation comes just 13 months after Mr Yousaf won the contest to succeed Nicola Sturgeon as first minister and SNP leader after narrowly defeating Kate Forbes in what had been a fractious leadership race.
Mr Yousaf, who became visibly emotional during his resignation speech, said: "I cannot tell you what an honour it is being the first minister of the country I love, the country I am raising my family in and the only country I will ever call home."
He added: "As a young boy born and raised in Scotland, I could never have dreamt that one day I would have the privilege of leading my country. People that looked like me were not in positions of political influence, let alone leading governments when I was younger. We now live in a UK that has a British Hindu PM, a Muslim mayor of London, a black Welsh First Minister and, for a little while longer, a Scots Asian first minister of Scotland."
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