Before the game began, if I told you that the San Francisco 49ers would lose left tackle Joe Staley, wide receiver Dante Pettis and play with a hobbled right tackle Mike McGlinchey, most would have predicted a blowout in favor of the Los Angeles Chargers.

Yet, late into the fourth quarter, the 49ers had multiple chances to steal a win on the road with their backup quarterback C.J. Beathard leading the team. Coming into Sunday’s contest, the keys for a 49ers’ victory included a strong rushing attack and a “bend, don’t break” defensive effort, but Kyle Shanahan’s squad could not execute in either of those departments.

Running back Matt Breida only rushed for 39 yards on nine carries, while backup Alfred Morris only gained 14 yards on four attempts. It’s usually not a good sign when a team’s non-mobile quarterback is the second-leading rusher for the team. The 49ers only ran 21 running plays, in comparison to Beathard’s 37 passing attempts on Sunday. As currently constructed, Shanahan’s team isn’t constructed to win playing this style of football.

Robert Saleh’s group wasn’t productive on Sunday either, missing more tackles (2018 season’s unfortunate theme) and letting Chargers’ quarterback Phillip Rivers carve them up. It didn’t help that corner Richard Sherman and safety Jaquiski Tartt were not playing with various injuries, but it seemed like the 49ers were thoroughly outplayed on defense. A lack of a threatening pass rush, combined with poor tackling ability is a nightmare for a defensive coordinator.

As San Francisco prepares to host the win-less Arizona Cardinals next weekend, here are some key takeaways from the 49ers’ close loss in Los Angeles.

1. QB C.J. Beathard is playing an unsustainable brand of football.

Just scanning over the box score, it looks like Beathard had an above average performance, completing 23 of 37 passing attempts for 298 yards, including two touchdowns and two interceptions. The weirdest statistic on the box score is that Beathard only took one sack for a loss of 10 yards.

Huh? It seemed like the 49ers’ quarterback was constantly getting up from the ground and that his jersey was covered in green after the game ended, yet there was only one sack recorded.

While most 49ers’ fans will applaud Beathard for his toughness and resilience for getting up after every Chargers’ hit, he can’t continue to take those hits. As the NFL continues to make the game safer for their most prized assets, Beathard continues to put himself in harm’s way, opening himself for vicious hits.

In the second half, there was one hit that took the 49ers’ signal caller out of the game, allowing backup Nick Mullens to make a cameo appearance. A large contributor to poor protection can be attributed to injuries, as backup tackle Garry Gilliam had to step in for Staley and McGlinchey continued to play while he was clearly hobbled. The second side to this is that Beathard is holding onto the ball for a split second longer than he should. Waiting for his receivers to get open, the 49ers’ quarterback is allowing the pass rush to get a hit on him after releasing the throw.

I’m sure the 49ers’ brain trust would like to see the remaining 12 games include Beathard in the starting lineup to evaluate his future potential, but if this keeps up, he won’t make it to Week 17.

2. Kyle Shanahan continues to work coaching wonders with an under-manned roster.

As I said earlier, there was absolutely no reason for the 49ers to have only lost by two points to a significantly better roster and veteran quarterback on the road. The difference in this game? One sideline had Kyle Shanahan and the other had Anthony Lynn.

When push comes to shove, I know which head coach I’d rather have running my team. With San Francisco’s franchise quarterback and star running back out for the season, Shanahan hasn’t flinched, preaching the “Next Man Up” motto and coaching the team like there’s supposed to win games on Sunday.

This week’s game is a prime example of why Shanahan’s elevating the offensive roster beyond its capabilities. With multiple injuries along the offensive line, backup skill players in the starting lineup and a second-year backup quarterback, the 49ers managed to put up 20 points, 298 yards through the air and 76 yards on the ground.

While the media continues to praise counterpart Sean McVay for the job he’s done with the Rams – rightfully so — what Shanahan’s doing with a Swiss cheese-like roster can’t be ignored either.

3. TE George Kittle, not FB Kyle Juszczyk, is the real offensive weapon

Kyle Shanahan’s offense seems pretty straight forward from an outside perspective. Use the zone-running game to set up the play-action passing game. Who benefits the most in that style of offense? It’s the tight ends who get wide open in the flat and the middle of the field because of the run-play fake.

Former fifth-round pick George Kittle has exploded onto the scene as one of the best tight ends in the league. A dazzling performance that featured six catches for 125 yards, including an 82-yard touchdown catch and run.

When quarterback Jimmy Garoppolo was in the lineup, it seemed like his most comfortable target was Kittle and now with Beathard, that connection hasn’t skipped a beat.

Wideouts Marquise Goodwin and Pierre Garçon are inconsistent in their play, having a lot of boom or bust potential in their weekly output, but Kittle seems to be productive every Sunday.

The Iowa tandem carried their college connection into today’s game, as Beathard targeted Kittle eight times – the most of any 49ers’ receiver. As the season goes on, the trust and chemistry is only going to grow between the two.

If I was asked who the best skill player on the 49ers’ offensive roster was, I wouldn’t hesitate to respond: George Kittle.

4. LBs Reuben Foster and Fred Warner are the most athletic line-backing duo in the NFL — already.

Alright, before you claim that I’m making a bold statement after watching Foster and Warner through my homer-colored glasses, there’s some factual validity. During Sunday’s contest, Foster and Warner combined to make 17 total tackles, one tackle for loss and also one quarterback hit.

While Foster had a poor showing last week in Kansas City, missing six tackles, he had a bounce-back game in Los Angeles, flying all over the field and making his impact known. There were numerous plays where the former first-round pick blew up the Chargers’ running back and it seemed like the Alabama version of Foster was on full display.

On the flip side, Warner had some poor moments in coverage, but was stellar in run defense, leading the team in tackles on Sunday with 10. Warner was already among the NFL’s leaders in tackles and I expected him to stay near the top of the leaderboard, even with Foster returning to the lineup.

Carolina’s Thomas Davis and Luke Kuechly, Atlanta’s Deion Jones and De’Vondre Campbell, Seattle’s Bobby Wagner and K.J. Wright, and Minnesota’s Anthony Barr and Eric Kendricks are the other line-backing pairs that have similar athleticism to Foster and Warner.

Given their age and inexperience, I only expect the 49ers’ duo to improve as the year goes on.

5. The 49ers may have found an emerging contributor in S Antone Exum Jr.

While injuries ruin a team’s chemistry and rhythm, it also provides the opportunity for a practice squad player to immediately show off their ability to the team’s decision makers.

With starting strong safety Jaquiski Tartt unable to dress on Sunday, Robert Saleh and the defensive coaching staff turned to Antone Exum Jr., who delivered in the biggest way possible.

On the Chargers’ first offensive drive, Exum Jr. picked off Rivers and took it to the house for a touchdown – giving the 49ers’ their first defensive score of the season. Adding to that, Exum Jr. also had three tackles, three passes defensed and was around the ball in numerous plays.

While Tartt’s clearly the better player and will re-assume his starting position when he comes back from injury, Exum Jr. is a solid backup to have on the roster. Tartt’s brand of football gives way to lots of bumps and bruises and having Exum Jr. waiting in the wings isn’t the worst thing for Saleh.

6. WR Kendrick Bourne continues to impress in Year 2.

“Come for the touchdown, stay for the end-zone dance,” is how I’d classify Bourne’s season so far. After catching his first-career touchdown against the Lions, the ex-Eastern Washington receiver has followed it up with another reception for six points on Sunday.

Every week, I’m expecting a different end-zone celebration dance from Bourne after he scores a touchdown. Bourne finished the afternoon with three catches on four targets for 34 yards. He’s starting to solidifying himself as the third receiving option, after questions were raised about his roster spot with wideout Richie James Jr. emerging during training camp.

Bourne’s speed and strong route-running ability is allowing him to get open easily and make plays for the 49ers’ quarterbacks. With Pettis’ return time frame unknown, Bourne will continue to earn more playing time in the next few weeks.

While there were improvements on certain parts of the roster, the 49ers-Chargers game certainly had shades of 2017, with San Francisco competing for four quarters, but unable to close the deal in the waning moments of the game. Onto rookie quarterback Josh Rosen and the win-less Arizona Cardinals.