Kit can be used to measure the activity of genes in rice and related cereals, helping identify varieties with greater tolerance to drought, salt, climate, pests, or location
Agilent Technologies, in collaboration with Japan's National Institute of Agrobiological Sciences (Nias), has commercialised the first 60-mer oligonucleotide microarray for the study of rice, a staple food for half the world's population. 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 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% 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 1"x3" 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 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." Nias is an independent administrative research institute in Tsukuba, Japan, that maintains the world's most complete cDNA library of rice genes.
Its 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.
The sequences and annotations of these rice cDNAs, which correspond to approximately 22,000 unique expressed gene sequences, were recently published by Shoshi Kikuchi and coworkers.
Nias will provide cDNA clones to academic researchers upon request. "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 Takuji Sasaki, head of Japan's Rice Genome Research programme (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 ten nations and regions.
