An important step forward in aquaculture genomics

By Madelyn Kearns- November 20, 2020

New research highlights the possibilities that genetic variation in Atlantic salmon offers for advancing aquaculture production.

Spearheaded by Alicia Bertolotti, the new research involved sequencing the genomes of 492 Atlantic salmon in a project led by professor Dan Macqueen at the Roslin Institute (University of Edinburgh) in partnership with Xelect, the University of Aberdeen, and many international collaborators – including the Norwegian University of Life Sciences.

Published in the journal Nature Communications, the study is the first major investigation of its kind into structural variants in any farmed fish, Xelect – the project’s sole industry partner and contributing funder – said in a press release.  

Bertolotti accessed Xelect’s large archive of DNA samples and trait data for the study, with the company’s CEO Ian Johnston co-supervising her doctorate, completed at Aberdeen under the industrial CASE scheme of the UK’s Biotechnology & Biological research Council (BBSRC).

The study looked into different types of genetic variations in aquaculture production.

“The most common type of genetic variant distinguishing individuals of the same species are single nucleotide polymorphisms, or SNPs, which are differences in a single ‘letter’ of the DNA code,” Xelect said. “Structural variation is another major class of genetic variation, where large sections of the genetic code can be duplicated, inverted or even completely absent comparing different individuals.”

Concerning structural variation, fish farmers can glean a valuable tool as far as maximizing production gains goes, Xelect said.

“As structural variations are passed from one generation to the next, they provide another potentially valuable tool to use when maximizing production gains for fish farmers. Recent breakthroughs in computing power, bioinformatic algorithms and improvements in genetic sequencing technology have made it possible to identify structural variants, though this remains challenging,” the firm said.

One finding of note from the study, according to Bertolotti and Xelect, was “that many structural variations were located in brain-expressed genes that influence behavior.”

“Farmed salmon appear to have accumulated more of these variants than their wild relatives, presumably as a result of selective breeding for domesticated strains,” the press release stated. “There is clearly considerable potential for structural variations to increase trait gains using natural genetics.”

Bertolotti said the team faced some daunting challenges in its work.

“One of the greatest challenges we faced was filtering out the many false variants that were not true structural variations. None of the automated systems were accurate enough, so in the end we did it manually, which was an enormous task,” Bertolotti explained.

The research stands as an important milestone for aquaculture genomics, Xelect Operations Director Tom Ashton said.

“Alicia’s PhD and the resulting paper in Nature Communications represent an important step forward in aquaculture genomics, bringing us closer to being able to harness the power of structural variations in selective breeding programs,” according to Ashton.

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