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New Affymetrix Barley1 GeneChip Represents Another Fertile Field for Microarray Research

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Affymetrix last week introduced the Barley1 GeneChip array, a microarray created in collaboration with a global network of researchers organized by the US Department of Agriculture.

The Barley1 Genome GeneChip features over 22,700 sequences, including more than 1,000 genes from the National Center for Biotechnology Information non-redundant database, plus another 20,000 barley genes identified from 84 cDNA libraries representing various stages in the plant’s development. The array is manufactured to a feature size of 18 microns with 11 probe pairs per transcript.

For Affymetrix, Barley1 is the company’s second mass-market plant microarray product, and follows an Arabidopsis array rolled out in April 2002. Agilent, the No. 2 producer of commercial microarrays, has two catalog plant microarrays — Arabidopsis, introduced in 2001, and Magnaporthe grisea (rice blast), rolled out in May and produced in collaboration with a global research alliance that is similar to the group involved with the development of the barley array.

With two new plant microarrays released within the last three months by the industry’s manufacturing giants, both based on non-traditional model plants, and both constructed at the request of research groups, the industry is starting to harvest the agro-genomics field.

Barley, a grass with a cultivated history that goes back nearly to the roots of civilization, is an important medicinal and food crop that provides nutrition throughout its life cycle to both humans and animals. And, when its grains are moistened, sprouted, and roasted, it’s one of the principal ingredients in beer.

But don’t look for better Barley1 beer just yet. An Anheuser Busch spokesman told BioArray News that she was unable to locate anyone in the company’s agricultural research group who was comfortable enough with the subject of genomics to speak about it.

But, for those in the field, the microarray appears as enticing as a frosted mug on a hot day.

Joe Anderson, a genomics researcher at Purdue University, said barley is a good model system for other grains. Anderson said Purdue’s cereal-grain efforts center around wheat, which has a genome of 16 megabases and is unlikely to be fully sequenced any time soon. Barley will serve as a useful model system, he said.

“We undoubtedly will use the [Affymetrix] array,” said Anderson, a research molecular biologist with USDA’s ARS and an adjunct assistant professor in the plant pathology department at Purdue, “but we will use Nimblegen to create custom arrays using a series of genes that we have identified.”

Anderson said Purdue has facilities to analyze both GeneChips and 1’ x 3’ microarrays like those produced by Madison, Wisc.-based Nimblegen, but is not pursuing self-spotting: “We didn’t want to cross those technical hurdles,” he said.

Nimblegen, he said, will create custom arrays within hours, and will price them similarly to the catalog Affymetrix arrays, but will also allow tinkering with the content as needed.

Community Driven

Affymetrix representatives told BioArray News that the barley chip will sell at a price similar to that of the Arabidopsis array it sells.

Affymetrix designed and manufactured the Barley1 array for researchers in USDA’s Initiative for Future Agriculture and Food System’s Triticeae Improvement Group in a process that started with an idea a year ago and progressed rapidly, despite geography.

“The barley community is very close-knit,” said Lianne McLean, associate director of gene expression marketing for Affymetrix. “The reason that barley was able to move quickly [through the design and production process] was that the group was organized and open with their information.”

McLean said that when discussions first started, there were 50,000 barley ESTs publicly available. To participate, the researchers had to place their barley sequencing information in the public domain. Today, there are nearly 350,000 ESTs documented on NCBI’s dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html), ranking barley behind human, mouse, rat, Ciona intestinalis, chicken, and wheat, respectively, in number of ESTs available.

The barley group, McLean said, decided to make its array design widely accessible. Affymetrix will sell the chips in lots as small as five from a “small inventory available,” she said. “Corn, rice, tomato, and soy are high on the list” for future plant-content arrays, said McLean. “We are working and talking with other groups,” she said.

Timothy Close, a genetics professor at the University of California, Riverside, and the lead author on a paper documenting the Barley1 GeneChip and submitted to the journal Plant Physiology, said the Affymetrix product will provide large amounts of high-quality data.

“It’s much easier than I thought it would be,” he said. “I just provide chips, RNA, an account number and send it to UC-Irvine, and I get back a whopping amount of data.”

After a three-month testing period, the chips were introduced in late June.

— MOK

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