Norwegian selective breeding company Aqua Gen and researchers at the Norwegian University of Life Science's Center for Integrative Genomics, or CIGENE, hope to use a custom high-density Affymetrix genotyping array to improve the breeding of Atlantic salmon.
Aqua Gen, CIGENE, and Affy disclosed the development of the new tool in a statement this week. The HD array, which contains 923,627 SNPs from the Atlantic salmon, or Salmo salar, genome, has already been used to genotype 380 samples, according to Sigbjørn Lien, CIGENE's assistant director.
Lien told BioArray News this week that Aqua Gen and CIGENE had been using a 6,000-marker Illumina genotyping array in previous studies, but that recently available data from the ongoing sequencing of the yet-to-be published Atlantic salmon genome enabled them to resequence other salmon in order to generate a master set of about five million SNPs.
From that set, Aqua Gen and CIGENE selected the SNPs on the new high-density array. Lien said that Aqua Gen and CIGENE plan to genotype about a thousand animals with the HD array to select SNPs for a lower-density chip that will be used in future studies.
Based on initial genotyping of 380 animals, Lien said the researchers have already determined that more than 700,000 SNPs on the HD array are polymorphic and informative. Their ultimate goal is to produce an array with about 220,000 SNPs, "the amount for a useful product that will capture linkage disequilibrium." Lien said that the researchers aim to genotype about 7,000 salmon or more with this second-phase chip.
Nina Santi, director of R&D at Aqua Gen, told BioArray News this week that this second-generation high-density salmon array will be used to power genome-wide association studies that the company expects will yield markers that can be used to inform breeding decisions. She said that it is possible Aqua Gen might generate third-generation, lower-density arrays of about 60,000 markers for use in its programs. Acknowledging that using arrays in such a routine manner could be costly, Santi said that Aqua Gen is looking into developing "cost efficient" strategies to apply the technology.
The new HD array is essentially Aqua Gen's tool. The firm paid for the development of the chip, Santi said, and will continue to use it in house. CIGENE, which maintains a "strategic relationship" with Aqua Gen, will also be able to use the chip in research projects and collaborations. "This is not free for other breeding companies to use," Santi said of the firm's competitors, adding that it is "likely" that Aqua Gen's rivals will build their own genotyping chips.
Mindy Lee-Olsen, vice president of marketing at Affy, confirmed with BioArray News that the Santa Clara, Calif.-based vendor would not make Aqua Gen's chip available to other customers. She said that Affy has another salmon genotyping array design developed in a separate collaboration that it plans to make available as a catalog product next year.
According to Santi, Aqua Gen's main ambition is to identify markers associated with resistance to diseases and parasites that affect salmon aquaculture. The Trondheim-based company maintains a subsidiary in Chile, and will focus on lessening the impact of diseases – such as salmonid rickettsial septicaemia and the Pacific and Atlantic species of sea lice – that affect salmon in Chile and Norway. Santi noted that antibiotics are currently used to treat fish with SRS, while the salmon farming industry uses pharmaceuticals to combat sea lice, another impetus for using genetics to breed fish that are resistant to the diseases.
Aqua Gen has already had success implementing genetic marker-assisted breeding. Three years ago, the firm began supplying fish eggs selected for their genetic resistance to infectious pancreatic necrosis, a several viral disease of salmonid fish. In that amount of time, the national fish health statistics in Norway show a reduction of annual IPN outbreaks from 220 to 110 outbreaks.Based on that positive experience, the company "definitely thinks the new array will be a valuable tool," said Santi.
Aqua Gen's adoption of high-density genotyping arrays echoes similar moves by other animal breeding initiatives. For instance, at the Plant and Animal Genome conference earlier this year, researchers discussed a project called Dairy Genetics East Africa that has been relying on SNP chips to select the best-performing cattle breeds at sites in Kenya and Uganda (BAN 1/22/2013). The development of a high-density array for genotyping buffalo was also described at the same conference (BAN 1/22/2013).
Still, CIGENE's Lien noted that in comparison to cattle and buffalo, genotyping salmon can be more challenging. As he and fellow researchers noted in a 2010 Genome Biology paper, the common ancestor of salmon and trout experienced a whole-genome duplication, and modern species may be considered pseudo-tetraploid as they are in the process of reverting to a stable diploid state.
"SNP detection in salmon and other salmonids is quite different because the genome has been duplicated," Lien said. He credited the ability of Affy's genotyping software to automatically genotype non-diploid genomes with Aqua Gen and CIGENE's decision to use the vendor's products over its main competitor's. In a statement, Andy Last, executive vice president of genetic analysis and clinical applications at Affy, claimed that automatic genotype calling of non-diploid species enables data analysis to be completed in about one hour's time, regardless of the number of SNPs genotyped, "making it easier to meet tight breeding deadlines whilst also improving accuracy."
While breeding salmon that are resistant to diseases and parasites will be the main focus for Aqua Gen, Santi said that the HD array will also be used to aid in the assembly phase of the International Collaboration to Sequence the Atlantic Salmon Genome. "It will be made available for other scientific projects as well," she said. According to Lien, CIGENE plans to use the array to identify signatures related to genomic selection and environmental adaptation in wild salmon populations.