Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

viruses were injected to follicles on both wings for later studies. Chickens were raised in cages and observed on a daily basis over a two-month period. The regenerated feathers were plucked and examined with a dissection or scanning electron micrograph microscope for abnormalities compared with normal primary remiges. Histology and in situ hybridizationParaffin sections (5 mm) were stained with haematoxylin and eosin or prepared for in situ hybridization following routine procedures 26 . Cryostat sections (10 mm) were stained with X-gal. TUNEL staining was performed using a kit (Roche). Nonradioactive wholemount or section in situ hybridization or section in situ hybridization was performed according to the protocol described 22,26 . After hybridization, sections were incubated with an antidigoxigenin Fab conjugated to alkaline phosphatase (Boehringer Mannheim). Colour was detected by incubating with a Boehringer Mannheim purple substrate (Roche).

To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.

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Yeast artificial chromosome (YAC) clones were arranged on the positions of restriction fragment length polymorphism (RFLP) and sequence-tagged site (STS) markers already mapped on the high-resolution genetic maps of rice chromosomes 3 and 11. From a total of 416 and 242 YAC clones selected by colony/Southern hybridization and polymerase chain reaction (PCR) analysis, 238 and 135 YAC clones were located on chromosomes 3 and 11, respectively. For chromosomes 3 and 11, 24 YAC contigs and islands with total coverage of about 46% and 12 contigs and islands with coverage of about 40%, respectively, were assigned. Although many DNA fragments of multiple copy marker sequences could not be mapped to their original locations on the genetic map by Southern hybridization because of a lack of RFLP, the physical mapping of YAC clones could often assign specific locations of such multiple copy sequences on the genome. The information provided here on contig formation and similar sequence distribution revealed by ordering YAC clones will help to unravel the genome organization of rice as well as being useful in isolation of genes by map-based cloning.

SummaryA cosmid library of 3 • 10 .5 clones has been constructed from a human • hybrid cell line, 153E9a3, which contains human chromosome 2l (HC21) as the only human chromosome. From 56,500 clones of this library, 229 HC21-specific cosmids have been isolated by their hybridization to total human DNA and by their failure to hybridize to total Chinese hamster DNA. The cosmids isolated were then characterized, of these, 28 cosmids (12.2~ of those tested) contained Notl site(s), and 41 cosmids were localized on the eight subregions of HC21 by differential hybridization with Alu-PCR products obtained from a hybrid mapping panel. The cosmids localized were further integrated into the existing contigs using the end-specific probes of the clone insert. Therefore, they provided useful anchor points for contig mapping and walking.

Yeast artificial chromosome (YAC) clones were assigned on rice (Oryza saliva L. cv. Nipponbare) chromosomes 10 and 12 using DNA markers from our high-density linkage map. Out of 1,383 markers localized in this genetic map, 68 and 74 markers were located on chromosomes 10 and 12, respectively. Screening of the YAC genomic library was conducted by colony hybridization and Southern hybridization using restriction fragment length polymorphism (RFLP) markers or by polymerase chain reaction (PCR) using sequence-tagged site (STS) markers. We have completed the screening of 68 markers on chromosomes 10 and 74 markers on chromosome 12. A total of 134 and 103 YACs were assigned to chromosomes 10 and 12, respectively, with an estimated coverage of more than 60% for chromosome 10 and about 47% for chromosome 12. As rice is considered a model plant for genome analysis, the ordered YAC clones on chromosomes 10 and 12 as well as other chromosomes will certainly be helpful for isolation of agronomically and biologically important genes and for understanding the genome structure of these chromosomes.

Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.