SANTA CLARA -- On a day filled with difficult roster decisions, the hardest one shaped the 49ers' receiving corps for the coming season.

Wide receiver Bryan Gilmore, one of the team's fastest players and a long-time favorite of receivers coach Jerry Sullivan, was among 13 players released Saturday as the 49ers reduced their roster to the season-opening limit of 53.

The release of rookie running back Thomas Clayton was perhaps the biggest surprise. Clayton, a sixth-round pick from Kansas State, led the NFL in the exhibition season with 200 yards rushing. The 49ers could bring Clayton back when they form their eight-member practice squad today, provided he clears waivers.

Coach Mike Nolan said the depth at running back -- Frank Gore, Michael Robinson and Maurice Hicks were ahead of him -- made it hard for Clayton to land a spot.

The other players released include linebacker Colby Bockwoldt, tight ends Zachary Hilton and Zac Herold, defensive tackle Sam Rayburn, safeties Vickiel Vaughn and Darnell Bing, linebacker Mark Washington, tackles Harvey Dahl, Damane Duckett and Tavares Washington, and fullback Zak Keasey.

Gilmore, 29, had a strong camp and his ability to play special teams put him in the thick of the competition for a roster spot.

"Bryan is a consummate pro," Nolan said. "That was probably as difficult a decision as I've had in the two years I've been here. He's everything we're looking for in a player, but it was difficult because of the position."

But the team had upgraded the talent at receiver by acquiring Darrell Jackson in a trade and signing Ashley Lelie in free agency. Arnaz Battle stood out as the most productive returning receiver for the 49ers. Taylor Jacobs showed great improvement in camp, and Brandon Williams gained ground as a reserve receiver and punt returner. The team had invested a third-round draft pick in Jason Hill, who is still developing but has shown promise.

Gilmore traced his release to his lack of production last season, when he had eight catches as the third receiver while appearing in all 16 games -- three starts. His best game also was his last, making a catch and gaining 20 yards on a reverse to help set up the winning field goal in overtime in Denver.

"Basically, I had my chance and I didn't capitalize. That's the business," Gilmore said. "But they've got a good group at wide receiver and I look forward to the things they'll be doing this year."

Gilmore made a point of thanking Sullivan, who brought him to the 49ers a year ago after coaching him in Arizona and Miami.

"He gave me every opportunity, and I thank God for him and I thank him for everything he's done for me, for my family, and for my career," Gilmore said.

In related moves, nose tackle Joe Cohen (knee) and linebacker Jay Moore (ankle), both fourth-round draft picks, went on injured reserve, finishing their season.

Cohen said he tore two ligaments -- the anterior cruciate and posterior cruciate -- in his right knee when he was caught in a pileup Thursday in San Diego. He also sprained the medial collateral ligament.

Team doctors want to wait for the swelling to go down before scheduling surgery, he said.

"It's disappointing and humbling," Cohen said. "Pat Willis told me before the game, 'Play every play like it's your last.' You hear that and you're like, 'Yeah, whatever, Pat.' But that's really how the game goes. Luckily, this isn't going to be my last play. It's just going to be my last play for about a year."

Moore said an MRI exam showed no damage to bones in his ankle joint but muscle tissue, tendons and ligaments all had been "stressed." He faces a rehabilitation of six to eight weeks for the high-ankle sprain.

"It stinks. You make it all through camp and you get into the last preseason game and then something like this happens," Moore said.