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Ag-bio Researchers Designing SNP Chips for Plant and Animal Breeding as Sequencers Churn Out Data

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By Justin Petrone

The increased throughput and declining costs of next-generation sequencing are enabling more agricultural biotechnology researchers to obtain the information they need to design custom SNP-genotyping arrays for their organism of choice.

At the same time, scientists are opting for alternative genotyping approaches in their quest to better understand genetic variation and, ultimately, inform the breeding of more ideal plants and animals, according to several experts interviewed by BioArray News.

Array companies have long seen the value in selling catalog, organism-specific genotyping chips to ag-bio clients. Illumina, for instance, currently sells arrays for bovine, ovine, porcine, canine, and maize studies, and allows customers to design their own chips through its iSelect offering.

And Affymetrix jumped in the genotyping game last month with the back-to-back debuts of high-density genotyping chips for bovine and rice (BAN 1/18/2011). The firm similarly provides custom designs via its MyGeneChip program.

However, according to presentations at last month's Plant and Animal Genome conference in San Diego, many more ag-themed SNP chips are expected to become available soon, for organisms as diverse as wheat, horse, avocado, and catfish.

Some in the field directly attribute this coming wave of new ag-themed SNP chips to the availability of more affordable next-gen sequencing platforms.

"With next-generation technologies, survey sequencing of genomes is reasonably priced and the overall cost per data point has declined significantly enough to justify developing SNP chips," said Kellye Eversole, president of science and technology consulting firm Eversole Associates.

Eversole, who is also executive director of the International Wheat Genome Sequencing Consortium, told BioArray News this week that the IWGSC is designing a high-density wheat SNP-genotyping chip that could become available later this year.

She acknowledged that the wheat community has "been a little slower" than others, such as rice and maize, in developing such a chip, but attributed the slower pace to the "size and complexity of the bread wheat genome."

As of the middle of last year, the IWGSC had survey sequences for half of the 21 bread wheat chromosomes, achieved using Illumina and Roche 454 Life Sciences sequencers, she said.

The consortium is now in the process of completing survey sequences for the remaining chromosomes. These sequences will then be used to develop an IWGSC SNP array.

Eduard Akhunov, an assistant professor in the department of plant pathology at Kansas State University and an IWSWG coordinator, is leading the project to develop a 50,000-SNP-marker wheat-genotyping array.

Akhunov told BioArray News this week that the consortium has designed lower-density SNP chips, manufactured by Illumina, over the past few years, and is gearing up for a study that will use a 9,000-SNP array to genotype around 10,000 wheat lines this spring.

"This is the first public pilot project for testing the [Illumina] Infinium assay on wheat," Akhunov said. "If proven that it works, we plan to move ahead with developing a 50K Infinium assay," he said. Akhunov provided a tentative assay release date of summer 2011 for the 50K wheat chip.

Another plant-focused array that may be designed this year is for avocado. Luis Herrera Estrella, director of the National Laboratory of Genomics for Biodiversity in Irapuato, Mexico, said that he and fellow researchers are aiming to have a first draft of the avocado genome this year. Once that is achieved, the group's goal is to produce a SNP array for avocado studies and breeding. "Hopefully towards the end of the year we can have at least the design of the array," Herrera told BioArray News this week.

He said the SNP arrays will be "useful for us to carry out some studies about the origin and domestication of avocado in Mesoamerica, but probably more important is the use of the arrays by breeders to perform association mapping studies to characterize important agronomic traits."

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According to Herrera, the avocado has a long life cycle and it is a plant species in which directed crosses are difficult to achieve. He said the group has not decided about the manufacturer of the avocado SNP array but that Affymetrix is "certainly an interesting possibility."

Herrera added that his lab will do the assembly and annotation of the avocado genome in Mexico. He attributed the ability to make such arrays to improvements in sequencing platforms that have now made it "much easier, faster, and cheaper to generate sufficient SNP data to produce the arrays."

"I think one reason we may be seeing so many SNP arrays being developed for plants is that lots of plant groups have a reference genome and are now able to re-sequence diverse plant samples for SNP discovery," said Susan McCouch, a professor of plant breeding and genetics at Cornell University who led the development of Affy's GeneChip Rice 44K SNP-genotyping array, a 44,000-marker chip the vendor debuted last month (see BAN 1/25/2011).

The ability for consortia to re-sequence organisms via next-gen platforms is "giving everyone a real motivation to develop targeted SNP assays that are fast, economical, and easy to interpret, and can be used for lots of types of research and breeding applications," including diversity and evolutionary analysis, germplasm management, checking for seed purity, variety identification and fingerprinting, patent protection, and genome-assisted breeding applications," she told BioArray News this week.

"SNPs are much easier to use than [single sequence repeats], which preceded them, and the information can be readily databased so results of studies in different labs and on different species can be compared," said McCouch. "We've never had it this easy to evaluate genomic diversity, and I think there is a lot of interest in exploring the range of natural variation in plants these days."

While the rice community has welcomed the 44K chip, McCouch said it is already developing an even higher density array. She said that plant research communities are interested in designing SNP arrays to better understand "how plants adapt to a variable environment, the need for greater productivity and sustainability in food production worldwide, the search for new sources of biofuels and new perennial crop production systems."

All of these applications are now "really interesting and accessible because we suddenly have an efficient and cost-effective way of understanding genetic variation and thinking about how to better preserve, utilize, and generate new forms of it," she added.

Animals Advance

Like their peers in the plant research communities, scientists studying animals have embraced the ability to design SNP genotyping arrays for their organism of interest. Though the bovine community and others have led the way in seeing array technology adopted by providers that service breeders, such as NeoGen or DNA LandMarks, several other animal-themed chips are nearing completion.

One of these is for equine studies. Jim Mickelson, head of the equine and canine research lab at the University of Minnesota, said equine researchers are looking forward to the debut of a higher-density Illumina-made SNP chip next month.

"This is an Illumina array consisting of 74,000 assayed SNPs, with the customary caveat of at least 80 percent providing genotypes," Mickelson told BioArray News this week.

The SNPs were primarily identified in the National Human Genome Research Institute's horse genome project from seven discovery horses in addition to the equine reference genome sequence.

The previous version of the horse SNP array, called the Equine SNP50, contained around 56,000 functional SNPs. Mickelson said that that chip has been used for "gene mapping for traits of interest, both disease and performance traits, as well as population genetics parameters, equid and perissodactyl phylogeny, and now to detect genomic signatures of selection."

The production cost of the new SNP70 array has been financed by NeoGen. He said that the firm's GeneSeek subsidiary will begin offering genotyping services using the equine SNP70 by the middle of March.

Another animal-themed array that is advancing is for catfish studies. John Liu, director of the aquatic genomics unit at Auburn University in Alabama, said that the SNPs are currently being selected for a catfish chip and his research group soon plans to finalize a catfish genotyping chip containing around 50,000 SNP markers.

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"We have sufficient number of SNPs but their genomic spacing is under evaluation right now," he told BioArray News this week. "This chip will be built for all researchers and the catfish industry to use once available."

He added that he and fellow researchers are "evaluating the cost of the platforms and will make decisions soon as to which platform to use."

Horse- and catfish-genotyping chips are just two of many that are in various stages of development. At PAG, researchers discussed the development of a high-density SNP chips for studying chicken, lamb, goat, and cat, among other organisms.

Other Options on the Table

Though many plant and animal research communities have opted to move from resequencing of their organism of interest to developing genotyping arrays, others have decided on a different route, adopting lower-plex approaches to look at smaller numbers of SNPs.

Paul Arens, a researcher of ornamental breeding and genetic diversity at Wageningen University and Research Center in the Netherlands, told BioArray News this week that he and his colleagues have no plans to design SNP arrays for their studies.

Instead, Arens said the group is considering using Illumina's digital microbead-based BeadXpress system or KBioscience's KASP SNP genotyping system. The "numbers of SNPs and genotypes are still very modest and, besides, microarrays require quite some investment, which at the moment is not within our reach," Arens said.

Jinguo Hu, a molecular geneticist at the US Department of Agriculture's Agricultural Research Service, said that he too has opted for the BeadXpress over higher-density SNP chips.

Working together with researchers at the Genome Center at the University of California in Davis, he designed a 384 SNP panel for BeadXpress that he is using to "fingerprint the USDA lettuce germplasm collection for assessing genetic variation."

In Brazil, Marcos Machado at the Centro de Citricultura is using yet another platform for genome-wide genotyping in citrus. Machado told BioArray News this week that he last year began collaborating with Dart Technology in Australia, which sells a microarray platform called diverse arrays technology, or DART.

At the same time, he said, he and fellow researchers are weighing a move to a higher-density array-based approach

"We still do not have a SNP [array] platform since we did not have enough genomic information," Machado said. "However, after resequencing of three other citrus species, I believe we are really able to start thinking about using one."


Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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