Morris did not play this past weekend against the Houston Texans after joining his new 49ers teammates four days before kickoff. The team is without Jerick McKinnon (calf) and Matt Breida (shoulder) until Week 1 of the regular season.
Shanahan joined KNBR on Friday morning to discuss Morris and the running back situation.
"McKinnon and Breida, them being down and stuff has opened up a lot of reps for other guys," Shanahan said on the Murph & Mac show. "We got Jeremy (McNichols) a lot of reps last week. We're going to have Alfred start this game. He didn't get any carries last week, so I expect to see him a lot in the first half and see what he can do there.
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"All the other guys have gotten some opportunities. We'll mix them back in and spell Alfred out when he's tired in the first half. And we'll give the other guys who are up a go there in the second half.
"Joe Williams got hurt last week also, so he's not available. He may be available for next week in Week 4 but this game, starting out, is going to be Alf's game."
Morris already knew he would play against the Colts, but, as of Thursday afternoon, wasn't entirely sure when he would get into the game.
"That's up to the coaches, honestly," Morris said on 95.7 The Game. "If I start, great. If I don't, it doesn't matter to me. I will have an opportunity. I will play in this game, to my knowledge. Like I said, I'm thankful for this opportunity that I've been given so I can give myself a chance to make this team."
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