New genetic tools to speed the farming of Atlantic salmon are being made available for first time

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Development of single nucleotide polymorphism (SNP) markers.

New genetic tools to speed the breeding of Atlantic salmon are being made available to salmon farmers for the first time, with help from Breeding Insight, a new program funded by the U.S. Department of Agriculture (USDA) through Cornell.

SNP markers
Breeding Insight is a Cornell program that was set up to “elevate and support specialty crops and animal breeders in the USDA-ARS (U.S. Department of Agriculture-Agricultural Research Service) by developing genomics, phenomics, and data management tools for higher genetic gains outputs”.

Breeding Insight recently assisted scientists from the USDA Agricultural Research Service (ARS) in the development of single nucleotide polymorphism (SNP) markers, which are important tools for salmon farmers.

They said that the SNP markers are available for USA-based salmon farmers, such as Cooke in Maine and Pacific Aquaculture which has several steelhead net-pen farms on the Columbia River.

Until now, uniquely developed genomic resources for researching and breeding them were not publicly available, due to intellectual property constraints from competing commercial interests.

Milestones on the highway
“SNP markers are like milestones on the highway,” said Yniv Palti, USDA ARS research geneticist and lead on the project in a press release.

“These navigation points dramatically increase the speed at which breeders can select and introduce genes for traits that benefit fish farmers and consumers alike,” he said.

Palti explained that the goal is to bring the power of predictive breeding by enabling researchers to pinpoint sections of the genome associated with particular traits.

“By combining traditional breeding approaches with genomics and informatics, it is now possible to accurately predict some of the traits and performance of an individual long before it matures,” said Moira Sheehan, director of Breeding Insight.

“But the challenges facing specialty species such as salmon too often hamper technology adoption and limit program efficiency. Our goal at Breeding Insight is to level the playing field and create new opportunities for specialty crop and animal breeders to take value out of the genomics era,” she said.

Breeding Insight played a critical role in the salmon SNP marker project by providing expertise at the intersection of molecular biology and computing technology – a field more commonly known as bioinformatics.

Bioinformatics
“Bioinformatics is in such high demand. It’s the bottleneck for everything we do,” Palti said.

Palti said a consortium organised through biotechnology company The Center for Aquaculture Technologies (CAT) has committed to processing 50,000 copies of the SNP set (assembled on microscope slide-sized chips) as part of a genotyping service it offers.

CAT has an agreement with GM salmon farmer AquaBounty for it to use its patented sterility technology.

“Our primary goal is to generate resources that are being adopted by the aquaculture industry,” Palti said.