ABSTRACT
Rice (Oryza sativa L.) was the first crop plant to have its genome sequenced, and there were numerous reasons for this. Rice is consumed throughout the world more than any other cereal (FAO 2006). Nearly half of the people on the planet obtain nearly half of their daily calories from rice, and the demand for rice and all cereals is projected to increase with increasing global population and increasing affluence (Khush 1997; Gilland 2002). While global rice production continues to increase, global reserves of rice grain are declining (Childs 2008). Changing weather patterns are predicted to challenge the ability of rice producing nations to continue to increase production (Peng et al. 2004; Ohyanagi et al. 2006; Naylor et al. 2007). These agricultural facts made rice a candidate for genome sequencing, but biological considerations also favored choosing rice over other cereals. Based on flow cytometry, the rice genome has a calculated size of 415-439 Mb (Oryza sativa L. ssp. Japonica; Arumuganathan and Earle 1991). Of agronomically important grasses, rice has the smallest genome size. The experimentally calculated sizes of sorghum, maize, barley, oat and wheat are 772 Mb, 2.7 Gb, 4.9 Gb, 11.3 Gb and 16.0 Gb, respectively (Arumuganathan and Earle 1991). The
genomes of cereals are known to be highly colinear. Even after 60 million years of evolution, it is still possible to find fine-scale conservation of chromosome organization (Gale and Devos 1998). Thus, lessons learned from the analysis of the rice genome would be immediately applicable to other grass species. These are the types of reasons that rice was the first cereal genome to be sequenced, and in fact, rice has been the target of four separate genome sequencing efforts (Butler and Pockley 2000; Dalton 2000; Sasaki and Burr 2000; Dickson and Cyranoski 2001; Yu et al. 2002; International Rice Genome Sequencing Project 2005). These different projects have approached the problem of sequencing rice using different strategies and even different biological material. While the production of the rice genome sequence was impressive, the analysis of the rice genome has yielded an equally valuable resource. The computational analyses of the rice genome sequence have facilitated many facets of rice research from breeding to molecular genetics to phylogenetics to comparative genomics. This chapter will describe the sequencing of the rice genome and some of the computational analyses that have made rice genomic resources the focus of cereal genetic research for the last half dozen years.
