Washington DC - The Republicans in the Senate picked John Thune as the chamber's new leader Wednesday as lawmakers scrambling to prepare for President-elect Donald Trump's new administration rejected his camp's favored candidate.

Thune, who already holds a more junior leadership position, bested Texas Senator John Cornyn in a run-off to replace outgoing party leader Mitch McConnell, having already seen off Florida's Rick Scott, who was seen as most aligned with Trump.

The Senate – the upper chamber of Congress – jealously guards its independence and institutional authority, and its leadership election was seen as a clue into how much leeway members intend to give Trump.

Cornyn had the longer history in the chamber, while Thune was always seen as most aligned with the traditionalist wing of the party led by McConnell.

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Trump insiders had preferred Scott, an ardent loyalist who had promised to do the president-elect's bidding.

Trump's allies campaigned aggressively against Thune and Cornyn, pressuring individual senators in a push that has sparked a backlash – but Trump was wary of Scott's unpopularity and did not publicly endorse him.

Trump threw down a challenge Sunday to any prospective leader, demanding that they allow "recess appointments" – cabinet members that the president can name while the Senate is adjourned, bypassing the body's normal confirmation process.

Thune – along with the others – passed Trump's loyalty test by replying that he was open to the idea.

Scott's cheerleaders – a group that includes tech billionaire and Trump confidant Elon Musk, and far-right media personality Tucker Carlson – questioned Thune's commitment to the incoming president, dredging up past opposition.

Trump is expected to further test lawmakers with a series of controversial moves, not least pardoning many of the people convicted of crimes related to the 2021 storming of the Capitol.

Other members have winced at the incoming Republican's plans for steep, across-the-board import tariffs, although most are behind the president-elect's tax cut extension – which is expected to add significantly to the national debt.

The House and the Senate kicked off their frantic "lame-duck" session on Tuesday.

California is still counting ballots, but Republicans are widely expected to keep the House, handing the party total control of Washington after they claimed the Senate and White House last week.

The top priority for both parties in both chambers is funding the government to keep federal agencies open after December 20, with Republicans mulling a stop-gap measure that would keep the lights on into March.

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The extension would allow the Senate to begin to confirm Trump's cabinet members, and the House could focus on the president-elect's biggest priority – extending the 2017 Tax Cuts and Jobs Act before it expires in 2025.

Analysts are watching the House Republicans for how much of a deficit hit members are willing to swallow as they try to deliver their bill.

Republican House Speaker Mike Johnson said Tuesday he had been talking to Trump daily since last week's election, and the two met at a hotel in Washington early Wednesday, along with other party leaders.

The entire House – Democrats as well as Republicans – gets to vote on the speaker, meaning Johnson has to wait until the new Congress convenes in January to find out if he can secure the support of a majority of the chamber.

"Republicans in the House and Senate have a mandate, it's true. It was a decisive win across the nation," Johnson told reporters on Tuesday. "The American people want us to implement and deliver that America First agenda."