Understanding the rice plant by its genome sequence

• Main Authors: Sasaki, T, Matsumoto, T, Baba, T, Yamamoto, K, Katayose, Y, Wu, J, Sakata, K. (National Inst. of Agrobiological Science/Staff Inst., 1-2 Kannondai 2-chome, Tsukuba, Ibaraki (Japan). Rice Genome Research Program)
• Format: Conference Proceeding
• Language: English
• Published: Manila (Philippines) 2001
• Subjects: CHROMOSOME; CHROMOSOMES; CROMOSOMAS; GENE; GENES; GENETICA; GENETICS; GENETIQUE; GENOMAS; GENOME; GENOMES; NUCLEOTIDE; NUCLEOTIDES; NUCLEOTIDOS; ORYZA SATIVA

Significant progress has been achieved in elucidating the rice genome structure and function since the national rice genome project was launched in Japan in 1991. After 7 years, a fine molecular genetic map with 2275 markers, a YAC physical map covering 65% of the rice genome and about 10,000 independent ESTs became available. These tools opened the door for cloning genes behind specific traits. For further understanding of the rice plant from the genetic or molecular viewpoint, the second phase of the genome project started in 1998 using these tools as resources. One of the major goals is to sequence the entire genome that will facilitate the groundwork for accompanying subjects of functional and applied genomics by genetics and reverse-genetics methods. This concerted approach in rice genomics is expected to revolutionize current insights on the relationships between genes and traits and finally to understand what mechanism controls the nature of heredity in rice plant. To accelerate the completion of nucleotide sequencing, the International Rice Genome Sequencing Project (IRGSP) was organized and 11 countries now share the sequencing of the 12 rice chromosomes after adopting common standards for sequence quality, annotation and sequence release policy. A rice japonica variety, Nipponbare was chosen as template for sequencing using PAC/BAC clone-by-clone shotgun strategy. Japan takes the lead in this effort and is in charge of sequencing chromosomes 1, 6, 7 and 8. As of April 2001, physical mapping of chromosomes 1 (47 Mb) has been almost completed and its finished sequence will be available by the end of 2001. The current progress of genome sequencing is accessible on the web (http://rgp.dna.affrc.go.jp/GenomeSeq.html) and detailed information on genomic positions and annotation of sequenced PAC/BAC clones is integrated in the database named INE (http://rgp.dna.affrc.go.jp/giot/INE.html)