The mare worked at Flemington yesterday but was found to have swelling in the lower sheath of her flexor tendon in the off side fore leg.
"Scans have confirmed that there is damage in this tendon and therefore Atlantic Jewel will be scratched from Saturday's Cox Plate," a release from Mark Kavanagh Racing said.
Atlantic Jewel returned from a previous tendon injury this preparation to win the Memsie Stakes, the Stocks Stakes, finished runner-up to It's A Dundeel in the Underwood Stakes and at her last appearance she coasted away with the Caulfield Stakes. "At this stage she will be rested and the owners [Coolmore] will make a decision on her future over the next few weeks," Kavanagh said.
To add to the confusion, Flemington trainers Chris Waller and Danny O'Brien made the surprise moves of accepting for the Cox Plate with Foreteller and Shamus Award.
For Baker, the news of Atlantic Jewel's defection wasn't welcomed, but the possibility it created was.
It's A Dundeel is the only horse to have defeated Atlantic Jewel, beating her fair-and-square in the Underwood Stakes at Caulfield a month ago and shaped as the clear danger to her in Saturday's race.
After a slight setback two weeks ago, Baker said It's A Dundeel had made a complete recovery from the foot abscess that kept him out of the Caulfield Stakes.
"We think he's tightened up a bit. He looks healthy and we're pretty happy with him," Baker said.
It's A Dundeel turned in one of the best performances of the public gallops at the Valley on Tuesday morning, easily getting the better of the handy mare Let's Make Adeal.
For Baker, the Cox Plate is shaping as the making of a horse whose only rival for top honours was Atlantic Jewel.
"He's shown how good he is. His Derby win in Sydney was spectacular," Baker said.
"The thing with him is that he does it all so easily, he's easy to train, nothing worries him.
"He's relaxed, he's got plenty of speed and he can stay."
One rival trainer who agrees with Baker is Gai Waterhouse who named It's A Dundeel as the danger to her runner Fiorente, even before Atlantic Jewel came out. "He's a very masculine, big strong colt, I'm very impressed with the horse. Murray's a lucky man to be training him."
Meanwhile, Manikato Stakes favourite Samaready has drawn barrier seven for Friday night's group one sprint at the Valley. Hong Kong star Lucky Nine will jump from gate four in the 1200m race.
Friday: R8: 12:00 Sportingbet Manikato Stakes, A$1,000,000, 1200m.- Lucky Nine (4), Buffering (10), Temple Of Boom (11), Bel Sprinter (1), Shamexpress (2), Moment Of Change (6), Rebel Dane (9), Sessions (5), Le Bonsir (8) 58.5; Samaready (7), Diamond Earth (3), Arinosa (12) 56.5.
Saturday: R10: 7.40 Sportingbet Cox Plate A$3,000,000, 2040m.- Green Moon (12), Happy Trails (2), Fiorente (15), Foreteller (9), Side Glance (1), Seville (10), Rekindled Interest (6), Puissance De Lune (8), Masked Marvel (5), Mull Of Killough (4) 59; It's A Dundeel (13), Super Cool (14), 57.5; Atlantic Jewel (7) (Scratched) 57, Long John (11), Shamus Award (3) 49.5.
- AAP
