The uncertainty that Penn State faced in the first half of this football season involved how the offense would perform in Mike Yurcich’s new system, and whether the defense was going to rebound from a rough showing the year before.

Now as the second half of the season gets underway Saturday against Illinois at Beaver Stadium, the uncertainty for the Nittany Lions deals more with injuries and, specifically, the number of games quarterback Sean Clifford will have to miss after taking a shot in the ribs from Iowa linebacker Jack Campbell.

In his meeting with the media last Wednesday night, coach James Franklin gave no indication of Clifford’s injury or status for the Illinois game, saying only, “He’s doing everything he possibly can to get back as soon as he possibly can and go from there.”

The Nittany Lions (5-1, 2-1 Big Ten) lost a significant part of their defense with the absence of 325-pound tackle PJ Mustipher. He will miss the remainder of the season after suffering a knee injury early against Iowa.

Other players who left the Iowa game and did not return were running backs Devyn Ford and John Lovett and safety Jonathan Sutherland.

Penn State’s bye week came at a fortunate time to give injured players a chance to heal and possibly be in the mix for Illinois. In the meantime, the discussions among Franklin and his coaching staff will concern personnel changes if the recovery period is prolonged.

After Illinois, the Lions play three current top-10 opponents in the final five weeks – Oct. 30 at Ohio State (announced Monday as a 7:30 p.m. kickoff), Nov. 13 at home vs. Michigan, and Nov. 27 against Michigan State on the road.

While Yurcich’s offense produced its share of explosive plays in the first half, the Lions rank only 71st of the 130 FBS teams in scoring (28.3 points per game) and 70th in total offense (396.7 yards per game). The defense is fourth in points allowed (13.8 per game) and 26th in total defense (312.7 yards per game), and has given up just six touchdowns in 19 opponents’ trips to the red zone.

The loss to Iowa didn’t knock the Nittany Lions out of Big Ten or playoff contention, but the challenges will be much greater without Mustipher. Additionally, the team will struggle without Clifford for as long as he is sidelined. With two running backs also possibly out, the depth at that position has weakened.

Some concerns starting the second half:

What if Clifford can’t play?

Redshirt sophomore Ta’Quon Roberson was thrust into a tough situation after replacing Clifford at Iowa and the numbers showed it – three points, 7-of-21 passing, eight false-start penalties. Franklin said Roberson and freshman Christian Veilleux will compete for the starting quarterback job this week against Illinois.

Yurcich has called the pair “awesome to coach” and “really passionate about becoming good quarterbacks.”

» READ MORE: Penn State’s inexperienced backup quarterback had tough sledding at Iowa

“Ta’Quan, the ball can really pop out of his hand, man,” Yurcich told reporters two days before the Iowa game. “He’s got really good explosion. He’s got a really good whip with his arm. Christian continues to get better every day. Fundamentally, he is still learning the game, but he’ll make some plays where you say, ‘OK, this kid’s got a bright future as well.’”

Who replaces Mustipher?

One of the Big Ten’s best defensive linemen, Mustipher leaves a gaping hole in the trenches. Redshirt sophomore D’Von Ellies replaced him against Iowa, then left the game with an injury but later returned. He likely will start against Illinois alongside fifth-year senior tackle Derrick Tangelo.

The position lost a key player when Franklin declared redshirt sophomore Hakeem Beamon “unavailable for the season” last month without commenting further. Redshirt freshman Coziah Izzard has played in all six games this season and will see increased time, and two other redshirt freshmen – Amin Vanover and Fatorma Mulbah – could be on deck.

Who’ll carry the ball?

In the season’s first six contests, the Nittany Lions’ five running backs combined to average 93.8 yards per game and 3.99 yards per carry. The team average rises to 128.3 when you add in Clifford.

Sophomore Keyvone Lee (204 yards) and junior Noah Cain (202) are the leading rushers and considered the chief contenders to get the highest share of playing time.

» READ MORE: Iowa's Kirk Ferentz: Fans booed Penn State injuries because they ‘smelled a rat’

“You’ll see a rotation and hopefully we can go with more of one particular running back than another because somebody gets hot or somebody’s in a groove and emerges as a No. 1,” Yurcich said. “If they all continue to improve, you’re going to consistently see an equal number of reps. I think that’s the best way to handle that situation.”

Receiving depth tested

The Nittany Lions’ three starting receivers – Jahan Dotson, Parker Washington, and KeAndre Lambert-Smith – accounted for 89 receptions, 1,136 yards, and nine touchdowns in the first half. But only three other wideouts caught a pass, eight to be exact, for 75 yards.

Lambert-Smith went out of the Iowa game with a first-quarter injury, but returned. Still, the drop from starter to backup at this position is rather steep. One of the reserves – Cam Sullivan-Brown, Marquis Wilson or Winston Eubanks (La Salle College High School) – must step up to give the coaches a reason to play them.