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Rice Genome review : Rice Genome review Sushama Salgaonkar M.Sc.part II 17-09-12

Introduction: Introduction The world’s first genome of a crop plant that was completely sequenced Rice-monocarpic annual plant that usually grows between 1 and 1.8 meters tall with long slender leaves 50–100 cm long and 2–2.5 cm broad.Its small, wind-pollinated flowers are characteristic of graes.The seed is a grain normally 5–12 mm long and 2–3 mm thick The rice genome is well mapped and well characterized, estimated 400 to 430 Mb.Japonica and Indica: Japonica and Indica three main varieties-Oryza sativa : Indica : variety is long-grained, for ex.Basmati rice, grown notably on the Indian sub-continent.Japonica : Japonica rice is short-grained & high in amylopectin(thus becoming “sticky” when cooked), and is grown mainly in more temperate or colder regions such as Japan.Javonica : Javonica rice is broad-grained & grown in tropical climates.Rice is a model cereal plant: Rice is a model cereal plant The small size of its genome(430 Mb)its relatively short generation time its relative genetic simplicity(it is diploid, or has two copies of each chromosome).easy to transform genetically.belongs to the gra family the greatest biodiversity of cereal crops

Institute which sequence the particular chromosome: Institute which sequence the particular chromosome Sr no.Rice sequence participant Chromosomes 1 Rice Genome R esearch Program(RGP)Japan 1,6,7,8 2 Korea Rice Genome Research Program(Korea)1 3 CCW(US)CUG(Clemson university)Cold spring Harbor University 3,10 4 TIGR –US 3,10 5 PGIR-US 10 6 University of Wisconsin-US 11 7 National Center of Gene Research Chinese Academy of science-china 4 8 Indian rice genome program-university of Delhi 11 9 Academia sinica plant genomic center(Taiwan)5 10 Genoscope-France 12

PowerPoint Presentation: Sr no.Rice sequence participant Chromosomes 13 Universidad fedral de Pelotas-Brazil 12 14 Kasetsant University –Thailand 9 15 MG Gill University –Canada 9 16 John innescenter –U.K 2

Milestone in rice genome sequencing : Milestone in rice genome sequencing 2)Feb 1998-IRGSP launched under coordination of RGP 1)Sept 1997 – Sequencing of the rice genome was initiated as an international collaboration among 10 countries 5)Dec 2002 – IRGSP finished high-quality draft sequence(clone-by-clone approach)with a sequence length, excluding overlaps, of 366 Mb corresponding to ~92%-RG 3)April 2000 – Monsanto Co.produced a draft sequence of BAC covering 260 Mb of the rice genome;95% of rice genes were identify identified 4)Feb 2001 – Syngenta produced a draft sequence & identified 32,000 to 50,000 genes, 99.8% sequence accuracy & identified 99% of the rice genes 6)Dec 2004-IRGSP produce the high-quality ’ sequence-entire rice genome;with 99.99% accuracy & without any sequence gap

Indian complete work on RG sequence : Indian complete work on RG sequence The IRGSP initiated Japan in 1997 and it got under way in 1998.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 Biology(DPMB), University of Delhi South Campus(UDSC)and the National Research Centre on Plant Biotechnology(NRCPB)and the Indian Agricultural Research Institute(IARI), New Delhi.PowerPoint Presentation: The Indian share of chromosome 11 has been equally divided between these two centres.It was known to carry several diseases resistant gene including in Xac1bacterial blight resistant gene-selected Finding: chromosome segment sequence by IARI involve-6.825 million bp & predicted 1005 gene –with unknown function

Methods: Methods Clone-by-clone Generate a genomic library endonuclease digest Ligation into BACs Transformation in E.coli Collection of clone DNA fragment result in genomic DNA library

PowerPoint Presentation: Shotgun sequencing Genome is broken into much smaller, overlapping fragment.Each fragment is sequenced Genome is aembled on overlapping sequencing Useful for sequencing small genome

Structure of rice chromosome: Structure of rice chromosome

Observation Table : Observation Table Organism type relevance Genome size Chromosome no.No.of predicted gene Organisation Year of completion Sequence method done Rice Oryza sativa.J aponica nipponbare Crop & model plant 466MB 12 35,000-50,000 IRGSP 2002 Shot gun Rice Oryza sativa.indica Crop 420MB 12 46,022-55,615 Beijing genomic institute 2002 Whole genome shot gun

Significant findings from the sequencing of rice genome : Significant findings from 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-40,000 genes(37,344 coding genes)One gene can be found every 9.9 kb, a lower density than that observed in Arabidopsis.29% in clustered gene families 71% putative homology with Arabidosis , 90% Arabidopsis genes have putative homologue with rice.2,859 genes unique to rice and other cereals

Application : Application Understanding-plant evolution & the differences between monocots & dicots Improve-efficiency of rice breeding.Improve-nutritional value of rice, enhance crop yield by improving seed quality, resistance to pests and diseases & plant hardine Development of gene-specific markers for marker-aisted breeding of new and improved rice varieties How a plant responds to the environment and which genes control various functions-plant

PowerPoint Presentation: Repetitive DNA is estimated to constitute at least 50% of the rice genome

References: References www.daodoc.com/wiki/Transposable_element