Relations between Prime Minister Justin Trudeau and then-Attorney General Jody Wilson-Raybould first began to fray in 2017 over concerns about her choice to fill a vacancy on the Supreme Court of Canada.

A year before cabinet discussions about a plea deal for Quebec engineering company SNC-Lavalin, Trudeau and Wilson-Raybould disagreed about her recommendation of Manitoba Justice Glenn D. Joyal, sources familiar with the matter tell CTV News.

Trudeau was concerned that Joyal wasn’t committed to protecting rights that have flown out of interpretation of the Charter of Rights and Freedoms, particularly LGBTQ2 rights and even abortion access, neither of which are specifically enshrined in the Charter.

Wilson-Raybould not only wanted Joyal named to the court to fill the vacancy left by Justice Beverley McLachlin’s resignation, she believed Joyal should replace McLachlin as the top court’s chief justice, a position that caused Trudeau to question his justice minister’s judgment, the sources said.

According to the Canadian Press, Wilson-Raybould wrote a 60-page memo to Trudeau advocating for Joyal.

Joyal issued a statement this afternoon confirming he applied for the seat on the court but said he later withdrew his name from consideration.

“Ultimately, I had to withdraw my application for personal reasons, due to my wife's metastatic breast cancer,” he wrote.

“I fear that someone is using my previous candidacy to the Supreme Court of Canada to further an agenda unrelated to the appointment process. This is wrong.”

It is unclear when Joyal withdrew his application.

Alberta judge Sheilah Martin was named to court in November 2017 and Justice Richard Wagner became chief justice.

The disagreement over the appointment casts new light on the erosion of the relationship between Trudeau and Wilson-Raybould that culminated in her move out of the Justice portfolio and appointment as Veterans Affairs minister earlier this year.

Wilson-Raybould, who later resigned from cabinet, has claimed she was subject to inappropriate political pressure from senior members of the government to grant SNC-Lavalin a remediation agreement to avoid criminal prosecution on corruption charges.

Wilson-Raybould denied to CTV News that there was any conflict over the Supreme Court appointment and said that the selection of a new Supreme Court judge is ultimately a decision for the prime minister.

“In this process there are typically CONFIDENTIAL conversations and communications -- back and forths between the PM and the AG on potential candidates for appointment,” she said in an email.

“I do however find it extremely worrisome why you are even asking such questions and where you received any such information. Commentary / reporting in this regard with respect to a SCC appointment(s) could compromise the integrity of the appointments process and potentially sitting Justices.”

Joyal is a former provincial Crown attorney who in 2011 was appointed to the position of Chief Justice of the Manitoba Court of the Queen’s Bench by Stephen Harper’s Conservative government.

The Prime Minister’s Office was concerned about views Joyal expressed in a speech to the Canadian Constitution Foundation’s Law and Freedom Conference in the January 2017, in which he discussed about the way courts were interpreting the Charter, ushered in by Trudeau’s father.

“It may be one of the bitter ironies of Pierre Elliott Trudeau’s Nation Building strategy of the 1980s, that despite the celebration and promotion of the Charter, it has led to an institutional imbalance that dilutes a source of Canadian distinctiveness,” he said in the speech.

Joyal argued for a rebalancing the relationship between the courts and legislative branch.

“I would hope and have every reason to believe, that this would signal the beginning of a true dialogue with the courts, where the resulting policies would, I suspect, reflect a traditionally pragmatic and uniquely Canadian mix of liberal and non-liberal values.”

His speech raised concerns that Joyal, if appointed, would be less willing to protect rights that are based on a broader interpretation of the Charter.

Joyal’s elevation to the chief justice of the Supreme Court would have been unusual, as the position is typically filled from current members of the court.

The Prime Minister’s Office declined to comment on the matter.

With files from Joyce Napier, CTV News Ottawa bureau chief