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At PAG, Affymetrix, Partners Unveil New High-Density SNP Chips for Wheat, Salmon, Maize, Rose


SAN DIEGO – By April 1, Affymetrix will commence shipment of four new high-density SNP genotyping arrays for wheat, salmon, maize, and rose research, as well as a lower-density array for wheat breeders.

The new product releases, featured during a company workshop at the Plant and Animal Genome conference held here this week, are part of the microarray vendors' ongoing overtures to the agbio community, a market segment that is driving, in part, sales of its high-throughput Axiom platform.

"The role of genomics in improving breeding in crops and livestock is now well established and is driving ongoing market expansion and adoption of genomics platforms," Affymetrix COO Andy Last told BioArray News at the conference. "Our technology is perfectly positioned to meet the needs of high-throughput, cost-effective routine applications across an increasing range of crops and livestock."

Affymetrix has been courting agbio researchers and breeders for many years. Each year at PAG, the company in its workshops profiles a new range of genotyping tools developed with collaborators. Last year, for example, Affymetrix discussed new catalog and consortium-designed chips for studying buffalo, wheat, and plant ornamentals.

To coincide with this year's conference, Affymetrix said in a statement this week that it has designed in collaboration with researchers at the University of Bristol in the UK a high-density wheat SNP chip.

Dubbed the Axiom Wheat Genotyping Array, the tool is being made available in Affymetrix's high-throughput, plate-based 96-format with 817,000 markers, and was designed for the University of Bristol as part of the UK Biotechnology and Biological Sciences Research Council-funded Wheat Improvement Strategic Program (WISP).

Affymetrix is now accepting orders for the array.

Gary Barker, who is affiliated with the University of Bristol and is part of a team that is overseeing the genotyping within WISP, discussed the project's aims during Affymetrix's workshop. According to Barker, the elite wheat germplasm that is used in developed countries has become homogenous enough that it is in danger of soon reaching a bottleneck.

"The genetic yield could potentially plateau," Barker told BioArray News after his talk, "so we need to draw extra diversity into the elite germplasm."

To accomplish this, WISP has three "pillars," each one managed through a different institution. Researchers at the John Innes Centre in Norwich are screening landraces, genetic lines of wild wheat collected from around the world, to select a smaller number to resequence and, eventually, breed into existing cultivars. A second is occurring at the UK National Institute of Agricultural Botany in Cambridge, where researchers are using stimulants such as caffeine to encourage the growth of new, synthetic hexaploid cultivars that can then be bred back into existing lines. At the University of Nottingham, WISP scientists are also working on ancestral introgressions, taking related crops, like rye, that have desirable traits, and reintroducing that diversity into wheat.

"Though it's not a natural cross, it can be persuaded to happen," said Barker, adding "we are aiming to have a whole panel of lines, each of which has got a little substitution."

The University of Bristol will genotype samples used in all three pillars on the new 817,000-marker platform. "We need to look at what kind introgressions we've got," said Barker, using that pillar of WISP as an example. "We may start off with a thousand plants, but we don't want to give the breeders a thousand plants, so after genotyping, we can say where the rye is located on the chromosomes and create a minimal set of lines and say that these are the best that represent all the different substitutions possible," he said.

To benefit the breeders involved in WISP, including RAGT, Limagrain, KWS, and Syngenta, Barker and his colleagues are also developing a 35,000-marker array based on the data from the higher-density wheat chip.

"From the breeders' perspective, the HD would be quite costly to run on thousands of individuals, so that is why we are going to cherrypick the best SNPs and make it available on this new chip," said Barker.

Affymetrix representatives said during the workshop that the 35K wheat chip should become available for wheat breeders in March, ahead of the growing season. The University of Bristol researchers are also developing a custom 35K array that will be used specifically to analyze new hybrids generated at the University of Nottingham, will contain progenitor SNPs to track introgressions, and should also become available in 2014, Barker said.

The potential for new arrays to emerge from the high-density wheat chip does not end there, though.

Shantanu Kaushikkar, director of product marketing for Affymetrix's Genetic Analysis business unit, told BioArray News that the firm expects other regional-specific wheat chips to emerge.

"US researchers might want to look at their cultivars and look at 35,000 SNPs that are relevant to the US population, so that would be another 35K chip," Kaushikkar said, "while somebody from India might want another 35,000 SNPs that are relevant to their populations."

The 'growing importance' of salmon

Researchers and breeders who are interested in Atlantic salmon will also be able to order a new, high-density, Affymetrix-made genotyping chip.

Affymetrix helped develop the Axiom Salmon Genotyping Array with Scottish researchers at the University of Edinburgh, Edinburgh Genomics, University of Glasgow, and University of Stirling, as well as Landcatch, a genetic breeding company focused on Atlantic salmon. The resulting array contains about 130,000 SNPs, and will become commercially available in March, according to Affymetrix.

Alan Archibald, deputy director of the U of Edinburgh's Roslin Institute, told attendees of Affymetrix's workshop that Atlantic salmon is of "growing importance," with 150 million tons produced annually, mostly in the UK, Norway, Chile, Canada, and Australia.

At the same time, he noted that making genetic improvements in the tetraploid species based on available resources, including RNA-seq data sets and a consortium-designed, Illumina-made 6,000-marker SNP chip, has been slowed by a high frequency of duplicated genes, and access restrictions, making it difficult for researchers to distinguish SNPs and paralogous duplications.

For these and other reasons, Archibald stressed that there was a need for a high-density Atlantic salmon chip.

"It is needed for the same reason you need it in cattle – it enables us to deliver genetic progress much more effectively, faster, and more accurately," Archibald told BioArray News.

Archibald described the SNP selection process during his talk, as well as a validation study that found that the majority of SNPs on the array segregated in farmed Norwegian and Scottish salmon, as well as wild salmon from Scotland, Norway, and Ireland. Archibald and fellow researchers are now engaged in a genome-wide association study of lice resistance in 800 samples, he said.

The new chip is not the first Affymetrix has designed for Atlantic salmon researchers and breeders. Last March, Affymetrix announced that it would develop a custom high-density chip to improve the breeding of Atlantic salmon for Norwegian selective breeding company Aqua Gen and researchers at the Norwegian University of Life Science's Center for Integrative Genomics (CIGENE).

Representatives of Aqua Gen and CIGENE told BioArray News at the time that they would use the 930,000-SNP chip to study resistance to sea lice in salmon, as well as other diseases, noting that the salmon farming industry uses pharmaceuticals to combat sea lice.

However, Aqua Gen and CIGENE's array was a custom project and has been made available only for their use, unlike the new chip developed by Archibald and his colleagues in the UK.

"The chip will be available to anyone who wants it," Archibald said. He noted that private breeding companies could still find the availability of such a catalog array useful. "A fairly large amount of the users will be academics, whose findings will get published," Archibald said. "That's a public good that they can benefit from."

Maize and rose

Affymetrix will make two other high-density arrays for agricultural research available in coming months. Kaushikkar said that the firm will soon begin shipping a 600,000-marker Axiom Maize Genotyping Array, developed in collaboration with a German consortium led by researchers at the Technical University of Munich and Helmholtz Zentrum München.

According to Kaushikkar, the new chip includes markers from worldwide cultivars, including temperate and tropical founder lines, elite lines, hybrids, and double haploid lines from landraces and teosinte, a grass found in Central America from which modern maize is believed to have been derived.

"This is a worldwide array," Kaushikkar said during the workshop, adding that it can be used to "build an application that is relevant to every cultivar around the world."

In terms of competition, Illumina does offer a maize-focused SNP array. The company introduced the 50,000-SNP chip in 2010.

One Affymetrix chip that has recently become available contains about 70,000 SNPs selected from tetraploid cut rose and garden rose cultivars. According to information provided by Affymetrix, the new Axiom Rose Genotyping Array was developed in collaboration with partners at Wageningen UR Plant Breeding in the Netherlands and the Institute for Plant Genetics at Leibnitz University in Germany.

The firm suggested that the new chip could be used in complex trait research, including the generation of polyploid linkage maps, identification of multi-SNP haplotypes in progenies and breeding material, and quantitative trait loci analysis for the discovery of marker haplotypes associated with important phenotypic traits, such as disease resistance.