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Mapping the future

06-Nov-2003

Agilent Technologies has commercialised the first 60-mer oligonucleotide microarray for the study of rice, a staple food for half the world's population. Working in collaboration with Japan's National Institute of Agrobiological Sciences (NIAS), researchers can use the Agilent Rice Oligo Microarray Kit to measure the activity of genes in rice and related cereal plants, helping them identify varieties with greater tolerance to drought, salt, cold climate or pests for planting in less arable lands.

The implications for the food processing industry are immense. Manufacturers could soon be working within geographical locations that were previously thought to be impossible to farm rice in. On top of that farmers should also be rewarded with higher returning yields than ever before.

 

The microarray includes genetic probes for more than 21,000 genes from the genome of Oryza sativa L. ssp japonica (cultivar Nipponbare), a strain of rice that is mainly cultivated in Japan. This is believed to be approximately 50 per cent of the total rice genome, currently estimated at 40,000 to 50,000 genes. Agilent manufactures the microarrays using ink-jet-based technology, which prints DNA in situ onto 3cm x 9cm glass slides to a length of 60 oligonucelotides. The 60-mer gene probes provide five to eight times greater sensitivity than 25-mer probes.

 

"This microarray is based on actual, biologically-expressed sequences (cDNA), not sequences predicted to be genes by computer," said Dr Shoshi Kikuchi, head of the Laboratory of Gene Expression at NIAS and leader of the Rice Microarray Project, a part of Japan's National Rice Genome Project. "After several validation experiments with Agilent custom rice oligo microarrays, we found that the signals were very clear and the reproducibility was very good. We believe the introduction of this microarray system to the scientific community will accelerate the functional characterisation of genes in rice and related cereal plants."

 

The NIAS is an independent administrative research institute that maintains the world's most complete cDNA library of rice genes. Their full-length rice cDNA sequences, upon which this oligo microarray is based, were collected and completely sequenced as part of the Rice Full-length cDNA Project.

 

"Agilent's rice oligo microarray will complement the rice genome sequencing effort particularly in clarifying the function of the more than 50,000 genes predicted to exist in rice," said Dr. Takuji Sasaki, head of Japan's Rice Genome Research Program (part of the National Rice Genome Project) and the International Rice Genome Sequencing Project.

 

The first draft of the rice genome sequence was published in 2002, making rice the second plant organism to have its genome sequenced. The first was Arabidopsis thaliana, a member of the mustard family commonly studied by researchers as a model plant system. Like Arabidopsis, rice is a model organism for plant researchers. Among cereal plants, it is believed to have one of the smallest genomes while possessing one of the largest sets of common plant genes. The rice genome has comparatively few duplications and redundancies compared to its fellow cereal plants (wheat, for example, has six copies of every chromosome).

 

The Rice Full-length cDNA Project is a joint collaboration of NIAS, Foundation of Advancement of International Science (FAIS) and RIKEN Institute, under the supervision of the Bio-oriented Technology Research Advancement Institution (BRAIN). NIAS carries out Japan's rice genome sequencing project in conjunction with Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), and also coordinates the International Rice Genome Sequencing Project (IRGSP), a collaboration between 10 nations and regions.

 

Agilent believes that independent studies support the firm's claim that the 60-mer oligo microarray system provides the highest accuracy of commercial gene-expression solutions. Agilent's catalogue microarrays are fully compatible with most commercial 3cm x 9cm glass-slide microarray scanners.

 

Agilent Technologies is a US-based global firm that specialises in communications, life sciences and chemical analysis. The company's 30,000 employees serve customers in more than 110 countries. Agilent had net revenue of $6 billion in fiscal year 2002.