Broken-leg Holden out for six weeks
The US international suffered the injury in a tackle with Manchester City's Nigel de Jong during his team's 2-1 friendly defeat by the Netherlands in Amsterdam on Wednesday.
"It's disappointing for Stuart because he's come into the team and done ever so well," said Coyle.
"He's a very good player, an international player and he has shown a real desire and hunger to do well for our club. In both games we saw his quality so it's a blow. The most important thing is he returns bigger and better."
Holden joined Bolton in January from Houston Dynamo and after making his way back from a previous minor injury has started the club's last two games, and Coyle is hopeful that the Scottish-born midfielder will be fit for the run-in - and the World Cup.
"We're erring on the side of six weeks, and if that is the case then he will be capable of playing the last part of the season for us and putting himself in the frame for the World Cup," said Coyle, who is in the process of extending Holden's contract, which was originally to the end of the season.
"We've already spoken with him and his representative to assure him he will be here for longer because of the belief I have in him, and the quality he has shown since he came to the club."
De Jong, who was booked for the tackle, says he acted without malice. "Such offences are part of football," he said on the Dutch FA's website.
"I went for the ball and got the opponent at the end. I had no evil intent. If the ball is between me and the opponent, you have to go in full. If you do not then the opponent takes you. And if you're scared in a game you get injured yourself."