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    The Rice Genome Project PDF

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    Nilpa Patel
    The International Rice Genome Sequencing Project (IRGSP) is a consortium of 10 publicly funded labs that worked to sequence the rice genome. In December 2004, the IRGSP completed sequencing the entire rice genome and made the high-quality sequence data publicly available. Rice is one of the world's most important food crops and a model plant for grasses. The rice genome provides insights into plant evolution, genetics, and traits important for improving rice yields and nutrition.

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    The Rice Genome Project PDF

    Uploaded by

    Nilpa Patel
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    The International Rice Genome Sequencing Project (IRGSP) is a consortium of 10 publicly funded labs that worked to sequence the rice genome. In December 2004, the IRGSP completed sequencing the entire rice genome and made the high-quality sequence data publicly available. Rice is one of the world's most important food crops and a model plant for grasses. The rice genome provides insights into plant evolution, genetics, and traits important for improving rice yields and nutrition.

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    The International Rice Genome Sequencing Project (IRGSP) is a consortium of 10 publicly funded labs that worked to sequence the rice genome. In December 2004, the IRGSP completed sequencing the entire rice genome and made the high-quality sequence data publicly available. Rice is one of the world's most important food crops and a model plant for grasses. The rice genome provides insights into plant evolution, genetics, and traits important for improving rice yields and nutrition.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    2K views3 pages

    The Rice Genome Project PDF

    Uploaded by

    Nilpa Patel
    The International Rice Genome Sequencing Project (IRGSP) is a consortium of 10 publicly funded labs that worked to sequence the rice genome. In December 2004, the IRGSP completed sequencing the entire rice genome and made the high-quality sequence data publicly available. Rice is one of the world's most important food crops and a model plant for grasses. The rice genome provides insights into plant evolution, genetics, and traits important for improving rice yields and nutrition.

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    © All Rights Reserved
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    of 3

    THE RICE GENOME PROJECT

    International Rice Genome Sequencing Project (IRGSP)


    The International Rice Genome Sequencing Project (IRGSP) is a consortium of publicly
    funded laboratories. I was established in 1997 to obtain high quality, map – based sequence of the
    rice genome. It is currently comprised of ten members: Japan, the United States of America, China,
    Taiwan, Korea, India, Thailand, France, Brazil and the United Kingdom. The IRGSP adopts the
    clone- by- clone shotgun sequencing strategy so that each sequenced clone can be associated with a
    specific position on the genetic map. It adheres to the policy of immediate release of the sequence
    data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice
    genome. The high-quality and map – based sequence of the entire genome is now available in
    public databases.
    Rice is one of the world’s most important food plants. It is a model plant for the grasses. It
    has important syntenic relationships with other cereal species. Rice is a monocarpic annual plant
    that usually grows between 1 and 1.8 meters tall. It has long slender leaves 50-100 cam long and 2
    – 2.5 cm broad. Its small wind-pollinated flowers are characteristic of grasses. The seed is a grain
    normally 5-12 mm long and 2-3 mm thick. Rice is the world’s first genome of a crop plant that was
    completely sequenced.
    Varieties of Rice
    There are three main varieties of Oryza sativa:
    i) Indica: This variety is long-grained, e.g., Basmati rice, grown mainly on the Indian
    subcontinent.
    ii) Japonica: Japonica rice is short-grained and high in amylopectin (thus becoming
    ‘sticky’ when cooked), and is grown mainly in more temperate and colder regions such as
    Japan.
    iii) Javonica: Javonica rice is broad- grained and grown in tropical climates.
    Rice a Model Experimental Crop
    Rice is a model experimental cereal plant belonging to the grass family. It has relatively
    short generation time. It has a much smaller genome and the greatest biodiversity of cereal crops. It
    has a high degree of collinearity with the genomes of wheat, barley and maize. Rice exhibits
    substantial conservation of gene order (synteny).
    ‘Gene, the blueprint of life’, is the most precious propriety in biotechnology and agriculture.
    Genome often allows prediction of gene position across cereals. Rice has a simple genetic system
    (diploid and disomic inheritance). It has enormous number of genes controlling agronomically
    important traits. Wide genetic diversity is present in the genus Oryza. The rice genome is well
    mapped and well characterized by small size of its genome, estimated 400 to 430 Mb. The rice
    genome holds fundamental information in its biological ‘power’ including physiology,
    development, genetics and molecular evolution.
    Milestone in Rice Genome Sequencing
    • Sept. 1997 – Sequencing of the rice genome was initiated as an international collaboration
    among 10 countries.
    • Feb. 1998 – IRGPS launched under coordination of RGP (Rice Genome Program) of Japan.
    • April 2000 – Monsanto Co. produced a draft sequence of BAC covering 260Mb of the rice
    genome; 95% of rice genes were identified.
    • Feb. 2001 – Syngenta produced a draft sequence and identified 32,000 to 50,000 genes,
    99.8% sequence accuracy and identified 99% of the rice genes.
    • Dec. 2002 – IRGSP finished high- quality draft sequence (clone-by-clone approach) with a
    sequence length, excluding overlaps, of 366 Mb corresponding to ~ 92% - rice genome.
    • Dec. 2004 – IRGSP produce the high-quality sequence- entire rice genome; with 99.9%
    accuracy and without any sequence gap.
    The size (in Mbp) and predicted number of genes for each chromosome from rice
    Chromosome Size (Mb) Predicted Number of Genes
    Chr 1 45.1 4467

    Chr 2 36.8 3011

    Chr 3 37.3 3197

    Chr 4 35.9 2679

    Chr 5 30.0 2426

    Chr 6 32.1 2342

    Chr 7 30.4 2507

    Chr 8 28.5 2286

    Chr 9 23.8 1618

    Chr 10 23.7 1724

    Chr 11 30.8 1834


    Chr 12 27.8 1870
    Mitochondria 0.491 96
    Chloroplast 0.135 159
    Total ~ 383 Mb 30216

    Indian participation on Rice Genome Sequence


    The IRGSP initiated in Japan in 1997 and the project estimated to cost about $200 million.
    India joined IRGSP in June 2000 and chose to sequence a part of chromosome 11. India has
    invested Rs. 48.83 crores for the “Indian Initiative for Rice Genome Sequencing” (IIRGS). The
    initiative is a joint effort by the Department of Plant Molecular Bio9logy (DPMB), University of
    Delhi South Campus and the National Research Centre on Plant Biotechnology (NRCPB) and the
    Indian Agricultural Research Institute (IARI), New Delhi. The Indian share of chromosome 11 has
    been equally divided between these two centres. It was known to carry several disease resistant
    genes including Xac1 bacterial blight resistant gene – selected finding: chromosome segment
    sequenced by IARI involve 6.825 million bp and predicted 1005 gene - with unknown function.
    Facts about the sequencing of Rice Genome
    • The rice genome is about 389 mb, 370.7 Mb has been sequenced, 18.1 Mb unsequenced.
    • Sequenced segment represents 99% of euchromatin and 95% of rice genome.
    • The rice genome has approximately 40,000 to 60,000 genes (37,344 coding genes).
    • One gene can be found every 9.9 kb, a lower gene density than that observed in Arabidopsis.
    • 29% in clustered gene families.
    • 2,859 genes seem to be unique to rice and the other cereals, some of which might
    differentiate monocot and dicot lineages.
    • Between 0.38 and 0.43% of the nuclear genome contains organellar DNA fragments,
    representing repeated and ongoing transfer of organellar DNA to the nuclear genome.
    • Repetitive DNA is estimated to constitute at least 50% of the rice genome.

    Application and Impact of Rice Genome Sequence

    • Understanding – plant evolution and the differences between monocots and dicots.
    • Improve efficiency of rice breeding.
    • Improve nutritional value of rice.
    • Enhance crop yield by improving seed quality, resistance to pests and diseases and plant
    hardiness.
    • Useful in identifying plant specific genes that can be potential herbicide targets.
    • Development of gene-specific markers for marker-assisted breeding of new and improved
    rice varieties.
    Reasons for sequencing Rice first
    • Importance as crop.
    • Largest food source for poor.
    • Feeds half of world’s population.
    • Demand likely to increase dramatically.
    • In Asia alone, demand will increase by at least 35%.

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