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Illumina to Debut MaizeSNP50 Chip, Low-Density Bovine Panel This Quarter

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This article has been updated from a version posted January 13 to include additional comments from TraitGenetics and the USDA.

By Justin Petrone

Illumina this quarter plans to expand its ag-bio play by launching a maize genotyping chip — its first crop-themed array — and a low-density, 3,000-marker bovine panel for use in cattle breeding.

Illumina researchers discussed the new chips at the Plant and Animal Genome Conference, held in San Diego week.

The disclosure follows Illumina's announcement that it has begun to sell a high-density Bovine BeadChip, which will begin shipping to early-access customers later this quarter, and more widely in the second quarter (see BAN 1/12/2010).

During two separate workshops at PAG, Illumina discussed its upcoming MaizeSNP50 BeadChip. Content for the chip was selected through a collaboration involving the US Department of Agriculture, Syngenta, INRA and TraitGenetics.. The 24-sample BeadChip, the first in such a format, is now available for pre-orders and will ship at the end of the quarter.

During one of the presentations, TraitGenetics CEO Martin Ganal said that future applications for the chip include genetic mapping, determining linkage disequilibrium, identifying markers in plant breeding, genome-wide association studies, and genomic selection.

"The maize chip is the first large-scale SNP array for plants," Ganal told BioArray News in a follow-up interview this week.

"Currently, there is no large SNP array for maize available," he said. "In order to get further into the genetic analysis of corn, it was important to develop a larger array with many SNPs."

According to Ganal, there are "a lot of different applications" for the new array, including high-resolution genetic mapping. "Maize is highly polymorphic, there's relatively little known about LD in various types of material, and SNP arrays can help you look at molecular marker diversity in maize more in depth than before," Ganal said. "It might also be possible to conduct GWAS for certain traits and what will really interesting is the ability to select individual plants based on the value of individual markers in a process called genomic selection."

Describing the 3K bovine panel, Curt Van Tassell of the USDA's Agricultural Research Service told BioArray News that it will likely be used in the dairy industry to select cattle for breeding prior to purchase.

Van Tassell said breeders have been using the BovineSNP50 for similar purposes. The low-density panel is expected to cost less than Illumina's Bovine HD and BovineSNP50 BeadChips.

"The big issue is cost. If we can impute SNPs without almost no loss in accuracy and cut the cost down to $40 or $50 per sample, that will increase adoption," Van Tassell said. Using the lower-cost 3K array, which does not have a list price yet, breeders could "potentially screen females for candidates of bull mothers and then young bulls and then, depending on the desire of the organization, they would either follow up with the 50K or the HD before they put a final purchase on one of those animals," he said. According to Van Tassell, the cattle industry has "bought into" SNP array technology and "there's been no looking back ever since." He said that one of the reasons that the cattle industry has been a leading adopter of SNP arrays is because the "population structure and the wide use of artificial insemination make it perfectly suited for this kind of technology."

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