Agilent Technologies has introduced the first whole-genome oligonucleotide microarray for the study of Arabidopsis thaliana, the primary plant model used in gene expression research.
The microarray will enable researchers to study the gene activity associated with various biological functions, stages of growth, and response to stress in Arabidopsis. The goal of such research is to improve crop yields; enhance the quality of plant fibers, foods, and other materials; and increase plant resistance to disease and drought.
The firm believes that using the Arabidopsis 3 oligo microarray kit will give scientists a better understanding of these processes in common crop plants such as corn, soybean, and cotton. And while researchers already have access to home-brew microarrays and a commercial array made by Affymetrix, Sean Coughlan, head of agricultural biotech research at Agilent, said that the firm’s new array marks an improvement over those products.
“This is the first whole-genome array based on the current version [of the sequence], which is TIGR version 5, of all the protein-coding transcripts, which are 26,000,” Coughlan said.
“I think even more excitingly, with the comparative genomics data we have, there are an additional 11,000 unannotated transcripts, which come from a combination of MPSS (Massively Parallel Signature Sequencing database of the University of Delaware), comparative genomics from TIGR, and also a thousand noncoding RNAs culled from the genome.”
All told, the new microarray contains 37,000 probes, representing all Arabidopsis genes of known function and related genes of interest, Agilent said.
For the Palo Alto, Calif.-based firm, the launch of the Arabidopsis microarray is viewed as a fairly important event. “Within the Ag-Bio department, [this launch] would be significant, both from the marketing standpoint and from a standpoint of being a cutting-edge research tool, and the academic market is fairly large,” Coughlan told BioArray News.
The company wouldn’t provide an estimate on the market size for the product but said that Arabidopsis is the largest plant science genome opportunity. A company spokesperson noted that the National Science Foundation, for example, is providing roughly $10 million in support of Arabidopsis research.
Although the new array can be used with any two-color scanner, Coughlan suggested optimal use would come with use of Agilent’s scanner. “It’s the most sensitive scanner in terms of detection limits, and it’s also the quickest in terms of automatic gridding and extraction of data,” he said.
According to Coughlan, the use of microarrays in agricultural biotech research is “relatively new, but it is becoming increasingly common.”
“There’s really been an explosion of interest in agricultural microarrays over the last two years,” he said. “That’s all driven by the availability of either good qua-lity EST sequences, and/or genomic data. For instance, the two best annotated higher eukaryotic genomes are Arabidopsis and rice.”
Arabidopsis has been a target of microarray research dating back to the early- to mid-1990s, and the utility of the technology in studying the plant is vast, according to John Quackenbush, an investigator with The Institute for Genomic Research.
“If I look at a large number of Arabidopsis plants, and look at the genes that are expressed, and if I have different strains of the plant that respond differently to heat or to flooding or to almost anything else you could imagine, you could start to look to see if there are signatures which may or may not be easily linked to the biology, but signatures that might be predictive of their final response,” he said.
Battling With Affy For Market Share
Agilent’s primary competition in the Arabidopsis microarray niche comes from Santa Clara, Calif.-based Affymetrix, which sells the GeneChip Arabidopsis ATH1 Genome Array.
An Affymetrix spokesperson told BioArray News that the firm was in discussions with the research community regarding its next-generation Arabidopsis microarray, which will enable analysis of gene expression at the exon level. The new microarray is expected to have roughly 6.5 million probes and will be launched in mid-2005, according to the spokesperson.
Other than Affy, “the other [Arabidopsis microarrays] are mainly home brew,” Coughlan said. “There is the Qiagen genome-wide oligo set, but those, of course, are merely oligos that are supplied for home brew.”
But a superior probe set may not be enough to get researchers to switch to the Agilent microarray. For example, although the probes for Agilent’s Arabidopsis microarray are culled from TIGR’s database, don’t expect Quackenbush’s team at TIGR to be using them.
“The arrays we’ve been using for Arabidopsis, we’ve been using for a few years, and they’re arrays that we make ourselves,” Quackenbush told BioArray News. “We have been working to optimize these applications and the protocols we have in the lab for a good five years. So, we have a very robust and reliable protocol, and we have driven the cost per assay down to about $60.”
But, he said that if scientists were starting from scratch in this type of research it might make more sense to buy a commercial array, given the time and capital investment it would take to get the research started.
Agilent already has commercially available microarrays for rice and rice blast, and company officials said there are several other microarrays for agricultural research use in its pipeline, although they declined to name which organisms are targeted.
In addition to the GeneChip Arabidopsis ATH1 Genome Array, Affymetrix sells arrays for barley, grape, and soybean. The firm plans to release several arrays by the end of the year targeting the agricultural research market, including chicken, bovine, pig, wheat, rice, and corn microarrays. It also is designing microarrays for tomato, cotton, and citrus.