Chapter Five - The First Monocot Genome Sequence: Oryza sativa (Rice)

Abstract The sequencing of the rice genome is one of the major achievements in plant science with direct impact on improving the staple food for half the world's population. The high-quality and precise map-based sequence of Oryza sativa ssp. japonica ‘Nipponbare’ provides a valuable resource for characterization of many biological processes with direct roles in agricultural productivity and offers great opportunities for comparative genomic studies among thousands of rice cultivars and between rice and other taxa. The most recently updated reference sequence, now referred to as Os-Nipponbare-Reference-IRGSP-1.0, consists of 37,869 loci including 35,679 protein-coding and 2190 non-protein-coding loci. The high-quality genome sequence and annotation of rice and Arabidopsis, which are widely accepted models for monocots and dicots, offer evidence on similarities and differences of the two major groups of higher plant species that could be used in understanding the most basic features that define a plant. The genus Oryza also includes a wide range of species of various genome sizes reflecting a diversity that could provide genetic resources for breeding improved cultivars. Comparative analysis of genome organization including the genes, intergenic regions and transposable elements within the genus Oryza may yield key insights into genome evolution, speciation and domestication.