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Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial artificial chromosome fingerprint-based physical map of the rice genome to facilitate the whole-genome sequencing of rice. Most of the rice genome (-90.6%) was anchored genetically by overgo hybridization, DNA gel blot hybridization, and in silico anchoring. Genome sequencing data also were integrated into the rice physical map. Comparison of the genetic and physical maps reveals that recombination is suppressed severely in centromeric regions as well as on the short arms of chromosomes 4 and 10. This integrated high-resolution physical map of the rice genome will greatly facilitate whole-- genome sequencing by helping to identify a minimum tiling path of clones to sequence. Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes.
INTRODUCTION
Rice is the principal food crop of half of the world's population and also serves as a crop research system to understand yield, hybrid vigor, and disease resistance. Rice has emerged as a model system for studying cereal genomics because of its small genome size (430 Mb) (Arumuganathan and Earle, 1991), syntenic relationship with other agronomically important cereal species (Bennetzen et al., 1998; Gale and Devos, 1998), and the availability of genome resources such as well-defined genetic maps (Causse et al., 1994; Harushima et al., 1998), an extensive collection of expressed sequence tags (ESTs) (Kurata et al., 1994; Yamamoto and Sasaki, 1997; http://rgp.dna.affrc.go.jp/), the TIGR Rice Gene Index (Quackenbush et al., 2000; http://www.tigr.org/ tdb/tgi.html), and a yeast artificial chromosome (YAC) map (Saji et al., 2001; http://rgp.dna.affrc.go.jp/publicdata/ physicalmap99/yacall.html).
Determination of the complete genomic sequence of rice is the objective of the International Rice Genome Sequencing Project (IRGSP) (Sasaki and Burr, 2000; http://rgp. dna.affrc.go.jp/cgi-bin/statusdb/seqcol lab.pl), which is led by Japan and involves Brazil, China, Great Britain, France, India, Korea, Taiwan, Thailand, and the United States. The IRGSP is using a clone-by-clone strategy to sequence the rice genome. This approach, which has proven effective for the human genome (International Human Genome Mapping Consortium, 2001; International Human Genome Sequencing Consortium, 2001), the Caenorhabditis elegans genome (Coulson et al., 1986), and...