While Jessica Allister was leading the once moribund Gophers softball program to its first No. 1 national ranking ever last season, boosters were nervous the coach might bolt for another reclamation project at her alma mater, Stanford.

On Tuesday, those fears came to fruition, when Allister tearfully said goodbye to Minnesota after accepting Stanford’s head coaching position.

Gophers athletic director Mark Coyle said he “aggressively” pursued an extension with Allister, even during the season, and was willing to make her one of the highest-paid coaches in the Big Ten. She made $160,000 last season in the final year of her contract.

“Like I told Mark when it all started, this has nothing to do with there not being what I need at Minnesota,” Allister said. “Minnesota’s wonderful. It just has everything to do with Stanford being home.”

Allister started at catcher for four seasons at Stanford and led the Cardinal to its past two College World Series appearances, in 2001 and 2004. She still holds the school record for games played (266) and served as a Cardinal assistant coach from 2007 to 2009.

Stanford’s program has since fallen on hard times, going 13-35 last year under Rachel Hanson, who left this month after three seasons. In steps Allister, who took over the Gophers in 2010, when they were coming off a 16-37 finish.

Allister spent seven years with the Gophers, culminating with five consecutive NCAA tournament appearances. Sara Moulton, who pitched the Gophers to their first NCAA super regional berth in 2014, called Tuesday a sad day for the program.

Asked whom Coyle should hire next, Moulton gave one name: Jessica Merchant, a Gophers assistant under Allister the past seven years and a former All-American shortstop for Michigan.

“I think she would do an awesome job,” Moulton said. “I’m assuming they’d go hard after her just because she knows everything.”

Coyle said he would immediately begin a national search, as players and parents started coming to grips with the Allister news.

“I’m a little bit in shock right now,” said Trent Lindaman, father of Kendyl Lindaman, the Gophers All-American catcher. “I knew Coach Allister would be presented that opportunity [at Stanford]. I think Minnesota is in better shape than that program right now, but I understand her motivation for leaving.”

As a freshman last season, Kendyl Lindaman shattered Gophers records for home runs (20), slugging percentage (.899) and on base percentage (.598). Trent Lindaman said he hadn’t yet spoken to his daughter about Allister’s departure but eased concerns that she might transfer.

“In my mind, it doesn’t change anything for Kendyl,” he said. “She committed to being a Golden Gopher, and part of that is the coaching staff, but more of it is the school and the program.”

With Lindaman and then-senior Sara Groenewegen leading the charge, the Gophers cruised to Big Ten regular season and tournament titles this season. They were 54-3 at that point, yet the NCAA selection committee still bypassed them for one of the tournament’s top 16 seeds and a chance to host a regional.

The Gophers went to the Tuscaloosa, Ala., regional and got knocked from the tournament after going 2-2, with both losses to No. 16-seeded host Alabama.

Allister insisted the NCAA’s decision did not affect her decision to leave.

“I hate that it happened in the same year,” she said. “I don’t think the ceiling has been reached [for the Gophers]. I think Minnesota is set up to be good for a long time.”

Coyle doesn’t believe the selection committee snub will make it harder to replace Allister.

“Obviously Jessica did such a wonderful job in her time here and has transformed that program,” Coyle said. “The number of phone calls I’m getting already about this job shows you where that program is.”