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In this article we will discuss about the current status and collaborative work on rice genomics.
Rice (Oryza sativa) is a model species for monocotyledonous plants, particularly for members in the grass family. With the completion of the Arabidopsis genome, plant biologist will have greater opportunity to assess the entire gene sequence of a plant for the first time and every possibilities of extending Arabidopsis strategies to other plant such as rice.
Year 2002 must be remembered as year of rice genome sequence. In April, a draft sequence of indica rice variety was published by the Beijing Genomics Institute (BGI, China). Similarly another company, syngenta, published a draft sequence of Japanica variety in the same month.
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In November 2002, two members of the International Rice Genome Sequencing Project (IRGSP), namely the Rice Genome Research Program (RGP, Japan) and the National Centre for Gene Research (NGGR, China) published high Quality Phase 3-sequences of chromosome 1 and chromosome 4 respectively.
For various reasons, rice display attractive candidate for its genome sequencing. Perhaps prime reasons for selecting rice as a model plant is due to its small genome sized compared with other members of the Gramineae family. The size of the rice genome is estimated to be 420-466 mbp.
This is approximately one half of the DNA content of Sorghum (760 mb) and 17%, 8.8% and 2.7% of the DNA content, maize (2,504 mbp) barley (4,873 mbp) and wheat (15,966 mbp). Factors responsible for reduction in rice genome are attributed to its diploid nature and reduced content of repetitive sequence in DNA. In addition, availability of genetic and molecular resources in rice tempted plant scientist to select this remarkable staple food of world.
Current Status of the Rice Genome:
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The present techniques employed by the International Rice Genome Sequencing Projects (IR GSP) are BAC (Bacterial Artificial Chromosome) or PAC (PI Artificial chromosome). In this approach overlapping set is identified that is contigous with the chromosome.
The BAC/PAC sequences are assembled individually and the entire chromosome is then assembled from the overlapping BAC sequences. The sequences for each BAC/PAC are then annotated for various gene functions and the available date is released to the public.
According to available data on rice DNA from Gen Bank, total of 65,681 entries (genes) comprising 28,282,731 bases of sequences have been submitted from the rice EST sequencing projects. Nearly 56.9 mb is the genome sequence survey division and is derived from BAC end sequencing. The official goal of the International Rice Genome Sequencing Project (IR GSP) was to complete the sequencing of Japonica variety by the end of 2008. In addition, US based agro giant monsanto has sequenced 3,391 rice BAC.
This company used Oryzae sativa spp. Japonica variety “Nipponbare”. Assessment showed that a file of 7,000 simple sequence repeats with flanking DNA and map location is available on website (see Monsanto website-www(dot)rice-research(dot)org). It was, however, assessed that both the Monsanta and the Syngenta sequences private data, which are not readily available outside of the companies because of intellectual property rights.
Collaborative Work on Rice Genomic:
The integration of sequence information with available genetic marker and other resources is imperative. This would accelerate researchers to utilize the data. This was evidenced in Arabidopsis Genome Initiative.
Generation of vast amount of rice genomic sequence data and its compulsion to integrate with other information from rice breeding, physiology and genetics is apparent. One of the most valuable tools in analyzing rice genomic sequences is the identification of repetitive sequence.
In order to identify it researchers constructed a rice repeat database using known, curated rice sequences available from Gen Bank. This curated database contains satellite DNAs, transposons, telomeric repeat sequences and rDNA sequences. The repetitive sequence was identified by MUMer and REPuter programs. The curated and the MUMer identified repeat databases can be searched on the TIGR Rice Genome website using BLAST.
Researcher from the Institute for Genomic Research, Maryland annotated 1.33 mb of rice genomic sequence from BACS on the lower arm of chromosome 10 and identified a total of 235 genes. The average rice gene is 2.2 kbp containing 3.9 exons and 2.9 introns. The density of rice gene is one gene per 5.7 kbp. Actual G/C content of rice differs in their coding region (59.1% G/C) (Table 25.4).
One of the main constraints with rice annotation is the lack of accurate gene prediction programs. Therefore, a special version of Glimmer M, known as Glimmer R, was tuned to recognise genes in the rice genome.
