In 2017, Marine Harvest, the world’s largest Atlantic salmon producer, transitioned its selective breeding program to full genomics implementation using Thermo Fisher Scientific’s Axiom genotyping technology. Since then, more than 60,000 fish have been genotyped. Through a combination of genome-wide association studies (GWAS) and genomic selection, the company’s breeding program has increased accuracy for trait selection in growth rate, disease resistance and product quality.
In a recent interview, Matt Baranski, Genetics Manager with Marine Harvest, describes the company’s process for ensuring the best-quality product possible. The company rears eggs and produces feed in-house. They use the most advanced tools available to make fish selection as accurate and as high quality as possible for their customers. As part of this approach, breeding plans focus on genomic selection for economically important traits.
According to Baranski, when he first started publishing genomics research, there was little interest from within the aquaculture industry. However, as technology has improved, producers are rapidly bringing molecular methods into their breeding programs. And they are meeting with success; genomics data help producers select for valuable traits that match species with husbandry environments.
In a workshop delivered to the World Congress on Genetics Applied to Livestock Production (WCGALP), Baranski further expands on why a genomic breeding program is so important in aquaculture.
All economic traits of importance in aquaculture have a genetic component. These include growth rate, feed conversion, flesh quality and disease resistance, in addition to sex selection and maturation indicators such as the puberty gene in salmon. Refining genetic evaluation to the level of individual fish increases accuracy in breeding values, moving from family traits to identifying individuals within families that show certain phenotypes. Increased accuracy in genotyping results means that breeders can select the best individuals for traits of interest.
The salmon genome was sequenced and published in 2015; it contains 3 Gb of information and around 46,598 genes. The data are complicated, since the genome is ancestrally duplicated. Marine Harvest developed genotyping arrays by mining existing RNA-Seq databases to cover major polymorphic high-resolution single nucleotide polymorphisms (SNPs) as informative markers. Ongoing product development in collaboration with Thermo Fisher Scientific has scaled up coverage, adding greater SNP coverage to each array.
Baranski reports good support from the Thermo Fisher bioinformatics team at all stages of research and development of the Axiom salmon genotyping arrays.
“We’ve been able to make our product better and better,” he says, “and increase the efficiency of our analysis pipeline.” With this support, Baranski notes that Marine Harvest can evaluate what is needed from the product so it evolves as new traits appear.
Furthermore, working with the Applied Biosystems Axiom genotyping solution saves costs by increasing scale and speeding up results. Not only can Baranski roll a wide number of analyses into a single test, but the genotyping workflow handles more samples. The bioinformatics pipeline has also accelerated to return results faster with higher accuracy.
“Now we can do everything in one step,” explains Baranski. “It’s really increased our efficiency as well as the accuracy of our data.”
If you would like to find out how Thermo Fisher Scientific agrigenomics solutions can help your breeding program, please contact us to arrange a free consultation with a genotyping expert
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