The scientific value of rice is further enhanced with the elucidation of the genome sequence of the two major subspecies of cultivated rice, cultivar Nipponbare was recently completed by a consortium of 10 countries, which comprised the International Rice Genome Sequencing Project (IRGSP), and represents a map-based finished sequence of the entire genome obtained using the hierarchical clone-by-clone sequencing strategy (Sasaki and Burr 2000).

The sequence of the cultivar was derived by a whole-genome shotgun sequencing approach (Yu et al. These genome sequences are invaluable resources not only in understanding the structure and function of the rice plant itself but also in deciphering the organization of other cereal genomes, which share an appreciable degree of synteny with rice (e.g., Paterson et al. A total of 370 Mb of finished sequence of PAC and BAC clones from rice, including virtually all of the euchromatic regions, revealed several characteristic features of the rice genome.

Together with their economic importance, the Poaceae are an attractive group for comparative genomics because they include many important crops with diverse native distributions and at least 35-fold variation in genome size (e.g., rice = 420 Mb; wheat = ∼15,000 Mb).

The independent domestication of rice in both Africa and Asia, sorghum in Africa, maize in America, and wheat in the Near East has provided an excellent study system in which to explore the genetic complexity of adapting plants to human use (for example, see Paterson et al. Recent efforts to characterize Poaceae genomes better are reflected in their expansion from 1% to about 6% of the DNA sequence resources in Gen Bank (Paterson et al. This is exemplified by the nearly finished sequencing of each of two subspecies (see below), supplemented by exploratory genome-wide efforts in maize (Whitelaw et al. 2005), and large EST and STS-based DNA marker collections for many others.

A draft sequence of the subspecies representing 4.2× genome coverage and comprising 103,044 scaffolds corresponding to 466 Mb (Yu et al.

2002) was recently increased to 6.28× coverage and further revised using the Syngenta Nipponbare whole-genome shotgun sequence data (Goff et al.

The purple alignment line of lg2CNS17 represents how sequences near 5′ exons align.

Exons were identified in genomic DNA for all three genes using the complete c DNA of lg2-m RNA (AF036949) and then masked.The economic and scientific importance of the cereals has motivated a rich history of research into their genetics, development, and evolution.The nearly completed sequence of the rice genome is emblematic of a transition to high-throughput genomics and computational biology that has also pervaded study of many other cereals. The cultivated cereals, members of the Poaceae family of the angiosperms, provide about half of the calories consumed by humans and a growing share of biofuel.At least three genomewide SNP discovery studies have been conducted, with marked differences in numbers and rates of inferred SNPs due to the use of different target sequences (low-copy vs. BAC-end) and different approaches to filter paralogs and artifactual SNPs from the respective data sets.Comparison of low-copy DNA across the entire sequences using short sequence alignments and stringent filtering criteria resulted in inference of 408,898 (Feltus et al.In addition to the assembled genomic sequences, public databases currently contain 386,487 rice ESTs (db EST release 031105).