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10/01/12 8:07 PM ET

Villanueva scratched from final start of season

TORONTO -- Carlos Villanueva's season has officially come to an end after he was scratched from Tuesday's start against the Twins.

Villanueva was supposed make one more outing before the end of the year, but instead that assignment will go to rookie Chad Jenkins. The reasons behind the move were partially because of Villanueva's high volume of innings thrown this season, plus the club's desire to get another look at Jenkins.

The decision was made against Villanueva's wishes, but the veteran right-hander said he was still understanding of manager John Farrell's line of thinking.

"We've been talking about it the last couple days," said Villanueva, who is 7-7 with a 4.16 ERA this season. "Obviously I'm a competitor, I want to be out there, but with the long season and the last three games not meaning anything for [Minnesota], for us, regardless of playoff contention, they said they want to get another look at Jenkins and I'm board with that."

Villanueva is set to enter free agency at the end of the year, and it has become more apparent with each passing week that he's unlikely to return. The 28-year-old served as a swing man with the Blue Jays, and has spent each of the past two years in both the bullpen and starting rotation.

An opportunity to earn a full-time starting job is Villanueva's top priority for the offseason, and that appears to be something Toronto is reluctant to guarantee. GM Alex Anthopoulos and manager John Farrell have both displayed at least some level of skepticism that Villanueva would be able to handle the rigours of a full season in that role.

Villanueva has never thrown more than 125 1/3 innings in a season, but his ability to step in following a series of injuries to Toronto's rotation helped solidify the Blue Jays' staff.

"I'm comfortable," Villanueva said of his stance heading into free agency. "When the season started, obviously we were in different circumstances. I had an opportunity in the middle of the season and I feel like I took advantage of it. ... Hopefully I will get a chance to start.

"I have trust in my agent that he is going to do a good job with the situation. For me, I worry about the part that I can control, which is going out here and prepare myself and do the best I can."

Farrell dismisses reports of friction with GM

TORONTO -- With the offseason rapidly approaching, Blue Jays manager John Farrell is still finding himself having to speak out against reports suggesting he could be headed to Boston at the end of the year.

Farrell was questioned on the subject matter yet again on Monday afternoon after a media report suggested the second-year manager currently has a contentious relationship with Toronto general manager Alex Anthopoulos.

A Boston-area reporter, citing an unnamed source, indicated the Blue Jays "are willing to let Farrell go to Boston as long as they're compensated, due to friction" between the coaching staff and front office.

"I think it's disrespectful when someone makes a comment when they don't truly know what's going on inside," Farrell said. "That's the most disappointing thing, and I don't know where some people come off as if they know what's happening between Alex and I, or what we would think is happening between a manager and a GM elsewhere. That's just irresponsible with the comments."

Farrell, who is under contract through the 2013 season, was first linked to Boston in 2011 before Boston reached an agreement with Bobby Valentine. The reports resurfaced when Valentine came under fire late this year, and for the most part Farrell has been loathe to publicly discuss the issue.

The ongoing storyline has been another twist in what has been a frustrating season for both Farrell and Anthopoulos. The year began with hopes of competing, but a series of devastating injuries derailed that plan by late June.

The roster has been in a state of flux ever since, and Farrell said that's just one indication that there can't possibly be any ill will between himself and the higher-ups in the organization.

"Alex and I have dealt with a lot of challenges this year, documented by the changes on our roster, we've had 54 different players come here," Farrell said. "The fact that there's that much change and that many challenges to respond to, our communication is frequent, even in the times we've scuffled, you have those conversations where things aren't always pleasant, based on the won-loss record at the time.

"[But] that comment is unfounded."

Encarnacion not in starting lineup on Monday

TORONTO -- Edwin Encarnacion was held out of the Blue Jays' lineup on Monday night because of tightness in his trapezius muscle.

Encarnacion was forced to depart Sunday afternoon's game against the Yankees in the seventh inning because of discomfort in his neck and shoulder.

The Blue Jays remain optimistic that Encarnacion will be able to play in at least one of the club's final two games, but it's too early to know for sure.

"Hopeful, but he's not ready to go today," manager John Farrell said. "It's the classic day to day."

Encarnacion entered play on Monday night just one home run behind Detroit's Miguel Cabrera and Texas' Josh Hamilton for the American League lead in homers, with 42. He also ranks tied for third in RBIs (110), fourth in slugging (.557) and OPS (.941).

The Dominican native has been even more impressive with two strikes. He leads the Majors with 21 homers once reaching that plateau in the count.

Gregor Chisholm is a reporter for MLB.com. Read his blog, North of the Border, and follow him on Twitter @gregorMLB. This story was not subject to the approval of Major League Baseball or its clubs.