While Arabidopsis microarrays have become a standard ingredient in the plant researcher’s kitchen, researchers around the world have been cooking up recipes for rice chips to study this recently sequenced cereal crop, a relative of other key agricultural plants such as wheat and maize.
About 500 million tons of each of the three crops are produced worldwide each year, said Xun Wang, director of functional genomics at the Torrey Mesa Research Institute, a subsidiary of Syngenta. “Rice is not only a model organism for wheat and corn, but also an important cereal by itself,” he said.
In April, Syngenta published the sequence of the rice genome in Science. But even before the assembly was completed, the company teamed up with Affymetrix last year to construct a single-chip rice microarray containing roughly 24,000 genes —about half of the estimated 40,000 to 50,000 rice genes — with 16 oligo probes per gene. Unlike Affy’s commercial chips, this one does not contain any mismatch probes. An update of this array, including about 40,000 genes and with a smaller feature size of 18 microns and fewer probes per gene, will probably be available this summer, said Wang.
The company runs about 3,000 chips per year at the moment, the majority of them Arabidopsis and rice arrays. Syngenta has also made its rice chip available to collaborating researchers from industry and academia. Overall, it has established about 50 collaborative rice projects, besides a large number of internal research projects. So far none of these have resulted in publications, but Wang said that several manuscripts have been submitted to journals.
As an example of how rice microarrays can provide potentially useful information for crop improvement, he cited a grain development project. The researchers found that 270 genes were co-regulated during this process, among them several dozen transcription factors, and a novel promoter element was overrepresented in these genes. “That’s very powerful,” Wang said, “because this gives you a handle [on] how you can regulate this group of genes rather than just one gene at a time.”
Why Rice Chips Taste Better than Arabidopsis
So what is the added value of rice microarrays over good old Arabidopsis chips? For a start, Arabidopsis is a dicot, whereas rice is a monocot, meaning that the genes of the two organisms are not entirely homologous. In fact, 80 percent of Arabidopsis genes are contained in the rice genome, but only about 50 percent of the rice genes are found in the weed. Yet, “since we understand more Arabidopsis biology than rice biology, it is easier for us to interpret data from Arabidopsis arrays than from rice arrays,” commented Wang. But rice is more similar to the other grass family members, which Western agriculture is most interested in. “We obviously really care about corn and wheat in the agricultural field, but those genomes are just too big for us to handle, and rice...is the right model system,” said Wang. Mainly because of its smaller genome size, it is the only cereal crop that has been sequenced to date.
Wang’s group also found the rice chips to be useful for probing the gene expression secrets of other grains: 91.3 percent of the rice gene probes cross-hybridized with maize genes, and 81.3 percent with barley genes. Moreover, the researchers have used rice chips for wheat experiments as well.
So is there still a need to make arrays for maize and wheat? Wang said that Syngenta is in fact currently debating whether or not to embark on a maize oligo array. Right now, the company manufactures two different maize cDNA microarrays, each containing 10,000 unique genes in duplicate. But “our rice chip looks quite good for maize as well,” said Wang. “We will see how much information we can get from the rice chip.”
Rice Chips Next Hot Dish?
While rice is an important model organism for cereal crops, the commercial potential of a rice chip does not seem to be clear yet. Affymetrix and Agilent said they were not currently planning to bring a rice microarray to market, and a Monsanto company spokesman said it does not even use rice microarrays internally. Some rice researchers, on the other hand, are definitely looking for a provider — if the price is right.
Hei Leung, a plant pathologist and functional genomics project leader at the International Rice Research Institute, who emphasized that he was not speaking on behalf of the IRRI, said in an e-mail interview that he “would like to see some technology companies [start] to offer affordable chips so that we can concentrate our attention to deal with the biology.” But providing the technology at prices affordable to researchers in developing countries might be a problem, he said, which is why “a public consortium approach to provide access is essential.” At the moment the IRRI, which focuses on research benefiting low-income rice farmers, provides cDNA rice arrays containing a subset of about 1,000 to 2,000 clones to its researchers through a network of international laboratories. The EST libraries come from various labs in the US and one in India, and several groups contribute to printing the arrays. But “since we are still a young network, our experience is limited,” cautioned Leung.
One of the oldest rice chips, though not less palatable, comes from Japan, which embarked on a rice cDNA microarray project in early 1999. The project is a joint effort of the country’s National Institute of Agrobiological Sciences and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries and involves 64 research institutions across Japan. As a member of a microarray technology access program of Amersham Biosciences, it receives many reagents as well as generation three and four spotters, said Shoshi Kikuchi, head of the laboratory of gene expression at the NIAS, in an e-mail interview. The project’s first rice array comprised 1,265 EST probes, but has since been complemented by a second array with 8,978 probes. With the progression of a rice full-length cDNA project launched in 2000, the probe clones will soon be replaced by the 3’ untranslated regions of full-length cDNA clones, of which 28,000 are currently available. The program’s researchers are also planning to produce oligo arrays, he added, using 60- to 70-mers, and to collaborate with US, Australian, and IRRI laboratories.