SANTA CLARA – Through the first four days of practices, Brian Hoyer has left little doubt of his standing as the 49ers’ starter and, unquestionably best option, at quarterback.

Coach Kyle Shanahan targeted Hoyer on the first day of free agency. And after he signed a two-year contract, Hoyer has been unchallenged on top of the depth chart. Hoyer appears to give Shanahan exactly what he wants with his ability to use a play-action setup to get the ball deep down the field.

“Before I got here, I didn’t know he could throw the ball that far,” 49ers wide receiver Pierre Garçon said.

Hoyer let the ball fly again and again on Monday. After two run plays to open practice, Hoyer used his play-action fake and unleashed a perfect pass 50 yards down the field. Wide receiver Aldrick Robinson was wide open but dropped the easy touchdown.

Later, Hoyer sent a pass that traveled 55 yards past the line of scrimmage to speedster Marquise Goodwin, who beat the coverage of Rashard Robinson for one of their many hookups since the opening of camp.

Shanahan wants to build a dangerous running game, which is a major key for him to get what he wants from Hoyer and his sneaky-strong arm.

There is still a lot of tinkering going on with the offensive line, but that unit might have the most responsibility to provide Hoyer with the support to push the ball down the field.

The line has to provide holes in the run game for Carlos Hyde and whomever else might have a role in the ground attack. The line must also be able to sell the run on play fakes to put some hesitation into the pass rush.


Ultimately, the pass protection must hold up or the general public may never see the big-play offense that Shanahan envisioned when he brought Hoyer aboard.

--The 49ers practiced without their top three safeties. Starters Jimmie Ward (hamstring) and Eric Reid (ankle) were out with injuries. Early in practice, Jaquiski Tartt sustained an injury to his left ribs area and did not return. His status for the remainder of the week is unclear. Vinnie Sunseri and Lorenzo Jerome took over as the safeties with the first-team defense, while Don Jones and Chanceller James lined up with the second team.

--Outside linebacker Jimmie Gilbert is out for the season after sustaining a torn ACL in practice Sunday, Shanahan said. Gilbert received a $12,000 signing bonus and $62,000 in guaranteed money as an undrafted rookie from Colorado.

--Rookie tight end George Kittle (hamstring), Reid (ankle) and cornerback Keith Reaser (knee) are listed as day-to-day with injuries sustained during Sunday’s practice. Offensive lineman JP Flynn is out indefinitely. The 49ers designated wide receiver B.J. Johnson as waived/injured and claimed receiver Tim Patrick from the Baltimore Ravens. If Johnson clears waivers he will revert back to the 49ers.

--Aldrick Robinson, who dropped a deep pass at the beginning of practice, concluded the day with a long touchdown pass from Matt Barkley against the coverage of veteran cornerback Will Davis.

--Cornerback Rashard Robinson got his hands on a Hoyer pass intended for Garçon. However, instead of batting the ball down, Robinson tipped it and Garçon made the catch 25 yards down the field along the left sideline.

--Receiver DeAndre Smelter made a nice catch to get both feet inbounds on a deep out on a pass from undrafted quarterback Nick Mullens.

--Aaron Lynch intercepted a Barkley pass that was tipped by Quinton Dial at the line of scrimmage. Lynch also had a would-be sack on a play in which C.J. Beathard went ahead and completed a deep pass down the field for Goodwin.

--Rookie linebacker Reuben Foster recorded his third interception in four days. Shanahan explained why it was his favorite of Foster’s picks.

--The 49ers have their first day off from training camp on Tuesday. The squad returns to practice on Wednesday at 10:15 a.m.