Journal Article

From Mapping to Sequencing, Post-sequencing and Beyond

Takuji Sasaki, Takashi Matsumoto, Baltazar A. Antonio and Yoshiaki Nagamura

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 46, issue 1, pages 3-13
Published in print January 2005 | ISSN: 0032-0781
Published online January 2005 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pci503
From Mapping to Sequencing, Post-sequencing and Beyond

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The Rice Genome Research Program (RGP) in Japan has been collaborating with the international community in elucidating a complete high-quality sequence of the rice genome. As the pioneer in large-scale analysis of the rice genome, the RGP has successfully established the fundamental tools for genome research such as a genetic map, a yeast artificial chromosome (YAC)-based physical map, a transcript map and a phage P1 artificial chromosome (PAC)/bacterial artificial chromosome (BAC) sequence-ready physical map, which serve as common resources for genome sequencing. Among the 12 rice chromosomes, the RGP is in charge of sequencing six chromosomes covering 52% of the 390 Mb total length of the genome. The contribution of the RGP to the realization of decoding the rice genome sequence with high accuracy and deciphering the genetic information in the genome will have a great impact in understanding the biology of the rice plant that provides a major food source for almost half of the world’s population. A high-quality draft sequence (phase 2) was completed in December 2002. Since then, much of the finished quality sequence (phase 3) has become available in public databases. With the completion of sequencing in December 2004, it is expected that the genome sequence would facilitate innovative research in functional and applied genomics. A map-based genome sequence is indispensable for further improvement of current rice varieties and for development of novel varieties carrying agronomically important traits such as high yield potential and tolerance to both biotic and abiotic stresses. In addition to genome sequencing, various related projects have been initiated to generate valuable resources, which could serve as indispensable tools in clarifying the structure and function of the rice genome. These resources have been made available to the scientific community through the Rice Genome Resource Center (RGRC) of the National Institute of Agrobiological Sciences (NIAS) to enable rapid progress in research that will lead to thorough understanding of the rice plant. As the next trend in rice genome research will focus on determining the function of about 40,000–50,000 genes predicted in the genome as well as applying various genomics tools in rice breeding, an unlimited access to rice DNA and seed stocks will provide a broad community of scientists with the necessary materials for formulating new concepts, developing innovative research and making new scientific discoveries in rice genomics.

Keywords: Keywords: Applied genomics — Database — DNA — functional genomics — Genome resources — Genome sequencing.; Abbreviations: BAC, bacterial artificial chromosome; CUGI, Clemson University Genomics Institute; EST, expressed sequence tag; IRGSP, International Rice Genome Sequencing Project; NIAS, National Institute of Agrobiological Sciences; PAC, phage P1 artificial chromosome; QTL, quantitative trait locus; RFLP, restriction fragment length polymorphism; RGP, Rice Genome Resarch Program; RGRC, Rice Genome Resource Center; RiceGAAS, Rice Genome Automated Annotation System; YAC, yeast artificial chromosome.

Journal Article.  6746 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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