Friday’s news on the linebacker front was not especially encouraging for the 49ers.

Patrick Willis, nursing a lingering sprained toe, missed practice for the third consecutive day. So did Dan Skuta (sprained ankle), who joined his teammates on the field for stretching but did not participate in the team’s final workout before traveling to New Orleans.

The 49ers listed Willis and Skuta as questionable for Sunday’s game against the Saints, but it seems unlikely either will play. That would keep rookie Chris Borland in the starting lineup in Willis’ spot and probably elevate Aaron Lynch into a starting role as Skuta’s replacement.

This magnifies San Francisco’s challenge against Drew Brees and Co. The Saints are No. 2 in the NFL in total offense and No. 3 in passing offense.

Borland, who stands 5-foot-11, could find himself matched up against 6-7 tight end Jimmy Graham at times.

“He’s hard,” 49ers defensive coordinator Vic Fangio said of Graham. “Do you have any ideas? It’ll be a mix of guys depending upon the coverage and where he lines up. It could be a corner-type, a safety-type, a linebacker-type. …

“Graham is going to have that height advantage over almost everybody who lines up on him, just like he does every week in the NFL for the most part. It’s a tough matchup.”

Marcio Jose Sanchez / Associated Press

Skuta struggled to walk after hurting his ankle in the fourth quarter of Sunday’s 13-10 loss to the Rams. He has made some progress since then, partly because of hyperbaric-chamber treatments in Los Gatos.

Even so, he did not sound confident about his prospects for Sunday. Asked if he could have played if the game were Friday, Skuta replied, “I couldn’t play very well. … I was able to run around today, but I wasn’t as fast as I usually am.”

The 49ers also listed cornerback Tramaine Brock (toe), defensive tackle Quinton Dial (eye) and wide receiver Brandon Lloyd (hamstring) as questionable for Sunday’s game.

Briefly: Head coach Jim Harbaugh acknowledged that linebacker NaVorro Bowman could rejoin practice in the next week or two. Bowman, coming back from knee surgery, worked on change-of-direction drills on the side Friday as the 49ers started practice. … Harbaugh on Borland: “It means so much to him. You see that in the way he plays, the execution, the effort. He’s acquitted himself very nicely.”