For Dr. Tiago Hori, director of aquaculture innovation at Atlantic Aqua Farms, the challenge of bringing targeted genotyping by sequencing (GBS) into aquaculture was making sequencing technology economically feasible. The solution that Dr. Hori found was the AgriSeq platform, and it is working wonders for Atlantic Aqua Farms.
How are you applying the Applied Biosystems AgriSeq targeted GBS solution?
Aquaculture itself was the main challenge that Dr. Hori and Atlantic Aqua Farms faced. “In a lot of livestock species, because the value of the animals is so high, genomic selection is done using arrays directly, using high-density arrays like Axiom,” Dr. Hori explains. “Because in aquaculture the value per animal is so low, we have to try to reduce the genotyping cost per individual.” This means finding high-value genomic targets and focusing closely on those, rather than using broad panels.
Atlantic Aqua Farms began using high-density Axiom arrays for their species when these were available, which allowed them to identify about 50,000 single-nucleotide polymorphism (SNP) sites that were meaningfully variable in their populations and provided reasonable genome coverage. They used these sites to build smaller, less expensive 384 arrays. Dr. Hori achieved an even greater cost savings by specializing even further, developing AgriSeq panels with the 2,000 to 3,000 most useful SNPs for each species.
Why use tailored AgriSeq panels?
To put it simply, Dr. Hori explains that “This platform is the only way to implement genomic selection in a feasible way in aquaculture.” AgriSeq creates the opportunity for lower-cost genotyping of a smaller number of SNPs than other arrays, providing a 1,000–5,000 SNP middle ground between low-density PCR methods and high-density but more expensive arrays. Being able to genotype a smaller number of SNPs of interest at lower cost allows Dr. Hori and his team to apply genomic selection to aquaculture species, especially emerging species that have not been in aquaculture for as long as more established species that, as he put it, “that don’t have the same resources available as Atlantic salmon.”
What were your key findings from using AgriSeq technology for your work?
Dr. Hori was not worried about whether Axiom technology would work in his use case. Rather, his questions related to AgriSeq. “We were not really concerned about Axiom because the array was validated before by other groups, but we were a little concerned about how the AgriSeq platform would perform because some aquatic animals have very complex genomes.” Some fish can have up to 400 chromosomes and ploidy levels up to tetraploid, making their genomes a challenge for conventional animal genomics methods.
Despite their worries about calling and mapping errors, Dr. Hori’s team was able to work with Thermo Fisher Scientific to develop a few panels that could work with these complex genomes. The custom-designed panels worked well. Thermo Fisher Scientific’s Austin team “helped us through the bioinformatics of it. Our genome was too big to use the web platform for designs, so Thermo did the designs in-house for us,” Dr. Hori explains. “It was a good experience.”
How do you see this work evolving over time?
After their success creating AgriSeq panels for fish, Atlantic Aqua Farms is interested in bringing this process to shellfish, emerging species with very different genomes from fish and an even lower value-per-animal proposition. With this in mind, they hope for even smaller, more focused panels, perhaps 1,000 or even 500 SNPs in size, to find the tipping point at which the panel remains both small and comprehensive enough to economically inform genomic selection for more and more species. In Dr. Hori’s words, “In aquaculture, we are always going to be pushing for the least cost per genotype possible,” and Thermo Fisher Scientific is ready to help them make it happen.
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