Cox Plate favourite Atlantic Jewel has been scratched from the big race after sustaining a tendon injury during trackwork today.

The $2.80 star mare showed signs of swelling after her track gallop this morning at Moonee Valley and scans revealed damage to her flexor tendon.

The scratching throws markets into chaos, with It's A Dundeel the new favourite, slightly ahead of Fiorente and Puissance De Lune.

Connections of Atlantic Jewel are obviously devastated, but jockey Michael Rodd kept a positive face.

“It's been an amazing effort by Mark and the team to get her back and winning first-up after 18-months out and winning another Group I,” Rodd said.

“To have her come so close is very disappointing.”

The withdrawal of Atlantic Jewel will mean three year old Shamus Award will sneak into the capacity field. He joins the other three year old Long John at the bottom of the weights.