Skip to main content
Premium Trial:

Request an Annual Quote

Are Agricultural Applications a Fertile Field for Microarray Industry s Growth?


With the 12th annual International Plant and Animal Genome Conference convening in San Diego this week, and the recent discovery of bovine spongiform encephalopathy in at least one US cow [see BAN 12/31/2003], the agricultural research industry may provide a fertile field in which to seed the future growth of microarray technology.

A glance at the list of the 83 exhibitors at the PAG conference indicates a strong agriculture interest among the microarray industry. The industry's leaders -- Affymetrix and Agilent Technologies-- are hosting presentations to the 1800 attendees, as are second-tier array players like Telechem International/ and Illumina. Others from the industry with a show presence include Axaron Bioscience, Axon Instruments, CombiMatrix, febit, MiraiBio, MWG Biotech, NimbleGen Systems, and Qiagen.

And, as if to amplify the point, Affymetrix said on Monday it will underwrite the design fees required to create novel plant and animal whole-genome microarrays, in a marketing effort it calls the GeneChip Consortia Design Program.

In its announcement, the company said that 12 new arrays are planned for release this year including, wheat, rice, poplar, corn, pig, cow, chicken, grape, soy, tomato, cotton, and citrus.

Competitors did not appear ready to follow Affymetrix's lead.

"Design fees, which are minimal, may apply for certain custom projects depending on the specifics of the bioarray desired by the researcher," Samraat Raha, vice president for Amersham's CodeLink product line, said in an e-mail message. " For many custom projects there are no design fees. One of the primary drivers for researchers in choosing CodeLink for standard or custom bioarrays continues to be the superior performance of the platform in terms of sensitivity and reproducibility. After all, if understanding the underlying biology is a researcher's key objective, they are interested in using the platform that is best for consistently studying the activity of low abundance/low expressing genes."

"Our pricing is extremely competitive," said Scott Harrison, ag biotech industry marketing manager for Agilent's Life Science and Chemical Analysis unit. "We are seeking consortium relationships, but whether we waive or reduce design fees has an awful lot to do with the commercial potential of the organism. In those instances where we can team up with a consortium and move forward with a commercial product, it makes sense to be more aggressive. But, we consider our design fees to be very competitive."

Affymetrix did not respond to BioArray News requests for information on how consortia can qualify to have design fees waived and how the company is going to account for the uncollected fees.

A Vintage Year?

The first chip to emerge from Affymetrix's effort may be a grape genome microarray. John Cushman, professor of biochemistry at the University of Nevada, Reno, told BioArray News on Friday that the members of International Grape Genome Consortia had approved a final design for an Affymetrix array that will be manufactured within four to six weeks and then will be available for beta testing.

The GeneChip Vitis vinifera array, he said, will contain some 20,000 probes and will sell for approximately $300 to $350 per chip.

Cushman said that Affymetrix's decision to underwrite the design fees motivated the group to work with the company to design this array.

"The design fee was $200,000, and we said that is too expensive, we can't afford it," Cushman said. "They made the smart decision, in my opinion, to waive the fee, which will be great for research groups. I think it was the right thing to do."

Cushman said he thinks this decision to waive the design fee will entice other consortia to create similar collaborative-effort arrays.

In this consortium collaboration, Affymetrix is not plowing new ground. The company this summer introduced its Barley1 GeneChip, a product created with a global network of researchers organized by the US Department of Agriculture (see BAN 7/9/2003). Similarly, Agilent rolled out a Magnaporthe grisea (rice blast) microarray (see BAN 05/02/2003) in May, which it produced in collaboration with Ralph Dean, the director of North Carolina State University's fungal genomics laboratory.

Sowing New Markets

The collaborative efforts these new microarray products represent are markets for chips, and that, in turn, represents potential increased sales and product revenues. In this, the 10th year of the commercial microarray industry, the research field has become relatively saturated and growth for the industry will have to come from new customers, some of whom might be making initial ventures into microarray-based research. With steady growth, the microarray industry could reach a significant financial milestone of $1 billion in estimated revenues this year.

For Pat Hurban, head of investigational genomics at Paradigm Pharmaceuticals, a Research Triangle Park, NC-based company that provides microarray analysis serv-ices on both the Affymetrix and Agilent Technologies platforms, the Affymetrix announcement is of significance.

"It's a really important move," he said. "A lot of work and research and development dollars have gone into creating [current model organism genome microarrays]. And, Affymetrix and Agilent have gotten pretty good at developing those arrays, and both have found ways to do it far less expensively than in the past."

Hurban said that one of the challenges the industry faces in 2004 is getting the technology accepted more widely than today's early adopters of the tools.

"Drug development has accepted the [microarray-based] research paradigm wholeheartedly, and the forward-looking agriculture companies as well" he said. "But, for others, [microarray-based research] doesn't have the same perceived utility or cachet."

One stumbling block may be the cost of doing array research, Hurban said.

"Microarray research is not something you can do on the cheap," he said. "And, one of the barriers to entry to doing microarray research has been the availability of a good [model organism] microarray."

In the past, the availability of those types of arrays depended on the genomic information available, and a sufficient market to justify the costs of production.

Genomes Coming Online

A potential road map for the next arrays to reach the top of researchers' wish lists can be found on the National Genome Research Institute web page that contains a prioritized list of genomes to be sequenced (see chart, page 4). Chicken, dog, and cow are listed as high priority for sequencing, joining the red flour beetle, and drosophila and various fungi. Meantime, some economically important genomes, such as the pig, are listed as moderate priority.

However, researchers are already seeking arrays just for these yet-to-be-completely-sequenced genomes.

Emile Nuwaysir, of NimbleGen Systems of Madison, Wis., a com-pany providing microarray-analysis services on its proprietary platform, said his company has contracts to conduct research on nine of 20 plants being sequenced by the Institute for Genomic Research. (See Researchers are inquiring about a number of the others, such as lettuce, grape and grapevine, and tomato.

"The explosion in sequencing has hit agriculture just as heavily, or more, than any other place," he said. "There are hundreds of economic-ally or scientifically important genomes being sequenced. We are moving as quickly as the sequencing [progresses]."

Nuwaysir said that big genomes, such as cow, pig, and maize, may not be completely sequenced and stable for years.

After an initial reference organism is sequenced, the next wave, he said, would then be to analyze variance between this one and others.

"You pick a species and sequence it, like, say, dog," he said. "Then it hits you, there are all these strains of dog. Or, take tomatoes; there are 150 commercial varieties of tomatoes. That is the next goal."

For the grape industry researchers involved in the Vitis GeneChip-brand array, Cushing said, the chip offers a tool for prediction.

"If you have this particular regime of plant care and cultivation practices, you get this profile with a gene chip. That, ultimately, will be predictive of wine quality traits, and that is the long-term goal," he said.

However, the fact that plant genomes are often more complex than finished animal genomes can make basic functional analysis an immediate challenge.

"Cereal grain [genomes] are rather polluted or messy, unlike mouse or human, which have compact genomes relative to plants," said Hurban. "Corn is littered with transposable elements. Many plants have undergone multiple genome duplications in the past. So there might be lots of copies of any particular gene. At this point, we are not in a position to say that one particular copy is functional, or all copies are functional."

The short-term challenge, he said, is to get a genome into an array format for interrogation.

A model organism like arabidopsis can function well for certain investigations, but ultimately, there is a need to be able to study the sequence of the actual organism, Hurban said.

-- MOK


National Human Genome Research Institute: High Priority Organisms in Sequencing Process



February 10, 2002

Gallus gallus (chicken)

February 10, 2002

Fungal Genome Initiative I: (Cryptococcus neoformans, Serotype A; Pneumocystis carinii (human and mouse); Coccidioides immitis; Aspergillus nidulans; Rhizopus oryzae; Coprinus cinereus; Ustilago maydis

February 10, 2002

Apis mellifera (honeybee)

February 10, 2002

Strongylocentrotus purpuratus (sea urchin)

February 10, 2002

Pan troglodytes (chimpanzee)

February 10, 2002

Drosophila yakuba

June 10, 2002

Bos taurus (cow)

June 10, 200

Canis familiaris (dog)

October 10, 2002

Macaca mulatta (rhesus macaque)

February 10, 2003

Drosophila simulans

February 10, 2003

Schmidtea mediterranea (planarium)

June 10, 2003

Tribolium castaneum (Red Flour beetle)

June 10, 2003

Drosophila ananassae, erecta, willistoni, grimshawi, mojavensis, virilis, persimilis, sechellia

June 10, 2003

Fungal Genome Initiative II: (Candida albicans; Candida tropicalis; Lodderomyces elongisporus; Saccharomyces cerevisiae)

June 10, 2003

Monodelphis domestica (laboratory opossum)

June 10, 2003

Saccoglossus kowalesvskii


The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.