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Colling was appointed to the role in late 2009 and has been with the union through plenty of upheaval over the past eight years.
Otago Rugby Football Union general manager Richard Kinley confirmed yesterday that Colling had resigned.
Kinley said the position would be advertised and a replacement would be sought.
Colling could not be reached for comment yesterday.
He took over from Ian Arthur eight years ago and has worked hard to get players to the union and also keep the best players from the region in the South.
In what is an increasingly competitive player market, which is getting younger, Colling helps oversee the academy programme, which develops young players both on and off the field into the demands of the sport at first-class level.
A former midfielder, Colling played one game for the union in 1998. He first started working for the union in Central Otago as a resource coach for a couple of years before moving to Dunedin with the player development role.
Colling came into the role just as Otago and the Highlanders were separating and going along different development pathways.
The franchise and union have come closer in the past couple of seasons, although they do not have any formal connections.
Player recruitment is very aggressive but Colling has done well to keep most of the promising players in Otago over the past few years and has also managed to draw players such as Tei Walden and Josh Ioane south.
Meanwhile, Otago prop Craig Millar has been linked with a move to Japanese Super Rugby side Sunwolves.
Millar, who turns 27 at the end of this month, has played for the Highlanders in 2014 and 2016-17 but had limited chances last season. He could not be reached for comment yesterday and his agent did not return calls.
He has played 10 games for the Highlanders over three seasons but appears to be behind Daniel Lienert-Brown and Aki Seiuli in the pecking order of loosehead props at the franchise.
The Sunwolves will be coached next season by former Highlanders coach Jamie Joseph, who will be looking to shake up the franchise, which has struggled in its first two years in the competition.