Clive Smith said Kauto Star was almost certain to be retired after he was pulled up in the Gold Cup.
The 12-year-old, twice a winner of the race and third last year, was never travelling before losing his place on the first circuit, and Ruby Walsh made a swift decision to call it a day.
"The horse seems well in himself, but I've had a word with Ruby," said Smith. "He said he jumped the first really well and the second really well, but when he went to the water jump he just stretched a bit and possibly felt a pain inside.
"Ruby didn't want to go on because of that - it was probably from the tumble he had two weeks ago.
"I think we probably will retire him. We said we wouldn't say anything today, but I think it's a very good bet we'll do that.
"What a great career he's had and he's been a wonderful horse. I've been so proud to own him and also the support of everybody has been absolutely tremendous.
"I would say it's 90% certain that he'll be retired. Someone will have to come up with a very good reason for me not to retire him."
Walsh confirmed: "I jumped the water and I wasn't happy at that stage. When Kauto Star couldn't lay up with Midnight Chase, I knew I was in trouble.
"I just went further and further back and I was struggling badly going to the fourth-last (on the first circuit).
"If horses could talk it would be a lot easier as they could tell you how they were feeling. If that was the case, half the horses I've ridden this week wouldn't have run."
Nicky Henderson said of the defeated champion, Long Run, and fourth-placed Burton Port: "I'm thrilled with my two boys and I have to give credit to the winners. JP is one of the stalwarts of National Hunt racing and Jonjo and AP are superstars.
"You have to say Long Run was not quite good enough on the day - he was always struggling to get to the pacemakers, but Sam (Waley-Cohen) rode a great race.
"I'd imagine they'll both got to Aintree, the three-mile race (Betfred Bowl) would be good for Long Run.
"I don't know about Burton Port, I'll have to talk to Trevor (Hemmings, owner) but you'd say there's no reason why he wouldn't go to the National as it's the only chance he'll get to run off 11st 7lb."
Sam Waley-Cohen added: "I'm very disappointed he didn't win, but I'm not disappointed in the horse - he's run all right. When landing over the last I thought his stamina might see it out, but it didn't."
McManus had never before won a Gold Cup, and was understandably jubilant. He said: "It's a very special day, a very special moment - for Jonjo, for AP and for their families. It gives everybody a great lift and I just feel very, very proud."