Grass Genomes Research Articles

Genome conflict in the gramineae

The genomes of grasses and cereals include a diverse and large collection of selfish genetic elements, many of which are fossil relics of ancient origin. Some of these elements are active and, because of their selfish nature and the way in which they exist to perpetuate themselves, they cause a conflict for genomes both within and between species in hybrids and allopolyploids. The conflict arises from how the various elements may undergo 'drive', through transposition, centromere and neocentromere drive, and in mitotic and meiotic drive processes in supernumerary B chromosomes. Experimental and newly formed hybrids and polyploids, where new combinations of genomes are brought together for the first time, find themselves sharing a common nuclear and cytoplasmic environment, and they can respond with varying degrees of instability to adjust to their new partnerships. B chromosomes are harmful to fertility and to the physiology of the cells and plants that carry them. In this review we take a broad view of genome conflict, drawing together aspects arising from a range of genetic elements that have not hitherto been considered in their entirety, and we find some common themes linking these various elements in their activities.

A rapid and efficient transformation protocol for the grass Brachypodium distachyon

A fast and efficient microprojectile bombardment-mediated transformation protocol is reported for the grass species Brachypodium distachyon, a proposed alternative model plant to Oryza sativa for functional genomics in grasses. Embryogenic calli derived from immature embryos were transformed by a construct containing the uidA (coding for beta-glucuronidase) and bar (coding for phosphinothricin acetyl transferase) genes, and bialaphos, a non-selective herbicide, was used as the selection agent throughout all phases of the tissue culture. Average transformation efficiencies of 5.3% were achieved, and for single bombardments transformation efficiencies of up to 14% were observed. The time frame from the bombardment of embryogenic callus to the harvesting of transgenic T1 seeds was 29 weeks and 25 weeks for the diploid and two tetraploid accessions used, respectively. Since the seed-to-seed life cycle is 19 weeks for the diploid and 15 weeks for the tetraploid accessions, our B. distachyon transformation system allows testing of both the T0 and the T1 generation as well as production of T2 seeds within 1 year.

Ancestral genome duplication in rice

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat.

In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S.

Comparative RFLP mapping has revealed extensive conservation of marker order in different grass genomes. However, microcolinearity studies at the sequence level have shown rapid genome evolution and many exceptions to colinearity. Most of these studies have focused on a limited size of genomic fragment and the extent of microcolinearity over large distances or across entire genomes remains poorly characterized in grasses. Here, we have investigated the microcolinearity between the rice genome and a total of 1,500 kb from physical BAC contigs on wheat chromosome 1AS. Using ESTs mapped in wheat chromosome bins as an additional source of physical data, we have identified 27 conserved orthologous sequences between wheat chromosome 1AS and a region of 1,210 kb located on rice chromosome 5S. Our results extend the orthology described earlier between wheat chromosome group 1S and rice chromosome 5S. Microcolinearity was found to be frequently disrupted by rearrangements which must have occurred after the divergence of wheat and rice. At the Lr10 orthologous loci, microrearrangements were due to the insertion of mobile elements, but also originated from gene movement, amplification, deletion and inversion. These mechanisms of genome evolution are at the origin of the mosaic conservation observed between the orthologous regions. Finally, in silico mapping of wheat genes identified an intragenomic colinearity between fragments from rice chromosome 1L and 5S, suggesting an ancestral segmental duplication in rice.

Construction and analysis of a BAC library in the grass Brachypodium sylvaticum: its use as a tool to bridge the gap between rice and wheat in elucidating gene content.

A BAC library of 30,228 clones with an average insert size of 102 kb was constructed in the grass Brachypodium sylvaticum. Brachypodium has a simple genome, similar in size and repetitive DNA content to that of rice, and is more closely related than rice both to the major temperate cereals wheat and barley, and to the forage grasses. The library represents 6.6 genome equivalents, implying a 99.9% probability of recovering any specific sequence. The library was arrayed onto two high-density colony filters, which were screened with heterologous DNA probes from rice chromosome nine and from syntenous regions of wheat, barley, maize and oat. The construction of Brachypodium BAC contigs revealed that synteny between rice, wheat and Brachypodium was largely maintained over several regions of rice chromosome nine. This suggests that Brachypodium will be a useful tool in the elucidation of gene content in agronomically important cereal crops, complementing rice as a "grass genome model".

English

  The recent advances in plant genomics have greatly influenced basic research in many agriculturally important crops. Along with the availability of complete genome information from the model grass species rice and the model legume species M. trucncatula, the functional genomics activities in other crop species will accelerate the genomics studies of forage and turf. Brachypodium distachyon was recently proposed as a new model plant for forage and turf grass genomics studies. The combination of bioinformatics and genomics will enhance our understanding of the molecular functions of forage and turf species. This review focuses on recent advances and applications of functional genomics for large-scale EST projects, global gene expression analyses, proteomics, and metabolic profiling, as well as the impact of functional genomics on improvement of forage and turf crops.   Key words: Functional genomics, forage and turf grasses, ESTs, microarray, proteomics, metabolomics, Medicago truncatula, legume.  

A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of </=50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny-in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.

A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus.

Grass genomes differ greatly in chromosome number, ploidy level, and size. Despite these differences, very good conservation of the marker order (collinearity) was found at the genetic map level between the different grass genomes. Collinearity is particularly good between rice chromosome 1 and the group 3 chromosomes in the Triticeae. We have used this collinearity to saturate the leaf rust resistance locus Rph7 on chromosome 3HS in barley with ESTs originating from rice chromosome 1S. Chromosome walking allowed the establishment of a contig of 212 kb spanning the Rph7 resistance gene. Sequencing of the contig showed an average gene density of one gene/20 kb with islands of higher density. Comparison with the orthologous rice sequence revealed the complete conservation of five members of the HGA gene family whereas intergenic regions differ greatly in size and composition. In rice, the five genes are closely associated whereas in barley intergenic regions are >38-fold larger. The size difference is due mainly to the presence of six additional genes as well as noncoding low-copy sequences. Our data suggest that a major rearrangement occurred in this region since the Triticeae and rice lineage diverged.

Sequence‐based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement

The completed rice genome sequence will accelerate progress on the identification and functional classification of biologically important genes and serve as an invaluable resource for the comparative analysis of grass genomes. In this study, methods were developed for sequence-based alignment of sorghum and rice chromosomes and for refining the sorghum genetic/physical map based on the rice genome sequence. A framework of 135 BAC contigs spanning approximately 33 Mbp was anchored to sorghum chromosome 3. A limited number of sequences were collected from 118 of the BACs and subjected to BLASTX analysis to identify putative genes and BLASTN analysis to identify sequence matches to the rice genome. Extensive conservation of gene content and order between sorghum chromosome 3 and the homeologous rice chromosome 1 was observed. One large-scale rearrangement was detected involving the inversion of an approximately 59 cM block of the short arm of sorghum chromosome 3. Several small-scale changes in gene collinearity were detected, indicating that single genes and/or small clusters of genes have moved since the divergence of sorghum and rice. Additionally, the alignment of the sorghum physical map to the rice genome sequence allowed sequence-assisted assembly of an approximately 1.6 Mbp sorghum BAC contig. This streamlined approach to high-resolution genome alignment and map building will yield important information about the relationships between rice and sorghum genes and genomic segments and ultimately enhance our understanding of cereal genome structure and evolution.

Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution.

Surveys for conserved noncoding sequences (CNS) among genes from monocot cereal species were conducted to assess the general properties of CNS in grass genomes and their correlation with known promoter regulatory elements. Initial comparisons of 11 orthologous maize-rice gene pairs found that previously defined regulatory motifs could be identified within short CNS but could not be distinguished reliably from random sequence matches. Among the different phylogenetic footprinting algorithms tested, the VISTA tool yielded the most informative alignments of noncoding sequence. VISTA was used to survey for CNS among all publicly available genomic sequences from maize, rice, wheat, barley, and sorghum, representing >300 gene comparisons. Comparisons of orthologous maize-rice and maize-sorghum gene pairs identified 20 bp as a minimal length criterion for a significant CNS among grass genes, with few such CNS found to be conserved across rice, maize, sorghum, and barley. The frequency and length of cereal CNS as well as nucleotide substitution rates within CNS were consistent with the known phylogenetic distances among the species compared. The implications of these findings for the evolution of cereal gene promoter sequences and the utility of using the nearly completed rice genome sequence to predict candidate regulatory elements in other cereal genes by phylogenetic footprinting are discussed.

CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements.

In comparison with retrotransposons, which comprise the majority of the Triticeae genomes, very few class 2 transposons have been described in these genomes. Based on the recent discovery of a local accumulation of CACTA elements at the Glu-A3 loci in the two wheat species Triticum monococcum and Triticum durum, we performed a database search for additional such elements in Triticeae spp. A combination of BLAST search and dot-plot analysis of publicly available Triticeae sequences led to the identification of 41 CACTA elements. Only seven of them encode a protein similar to known transposases, whereas the other 34 are considered to be deletion derivatives. A detailed characterization of the identified elements allowed a further classification into seven subgroups. The major subgroup, designated the "Caspar " family, was shown by hybridization to be present in at least 3,000 copies in the T. monococcum genome. The close association of numerous CACTA elements with genes and the identification of several similar elements in sorghum (Sorghum bicolor) and rice (Oryza sativa) led to the conclusion that CACTA elements contribute significantly to genome size and to organization and evolution of grass genomes.

Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley.

Comparative genomic analyses have revealed extensive colinearity in gene orders in distantly related taxa in mammals and grasses, which opened new horizons for evolutionary study. The objective of our study was to assess syntenic relationships of quantitative trait loci (QTL) for disease resistance in cereals by using a model system in which rice and barley were used as the hosts and the blast fungus Pyricularia grisea Sacc. as the pathogen. In total, 12 QTL against three isolates were identified in rice; two had effects on all three isolates, and the other 10 had effects on only one or two of the three isolates. Twelve QTL for blast resistance were identified in barley; one had effect on all three isolates, and the other 11 had effects on only one or two of the three isolates. The observed isolate specificity led to a hypothesis about the durability of quantitative resistance commonly observed in many plant host-pathogen systems. Four pairs of the QTL showed corresponding map positions between rice and barley, two of the four QTL pairs had complete conserved isolate specificity, and another two QTL pairs had partial conserved isolate specificity. Such corresponding locations and conserved specificity suggested a common origin and conserved functionality of the genes underlying the QTL for quantitative resistance and may have utility in gene discovery, understanding the function of the genomes, and identifying the evolutionary forces that structured the organization of the grass genomes.

Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat.

Retrotransposons are a principal component of most eukaryotic genomes, representing roughly 40% of the human genome and 50-80% of some grass genomes. They are usually transcriptionally silent but can be activated under certain stresses. Despite their considerable contribution to genome structure, their impact on the expression of adjacent genes is not well understood. The steady-state transcript levels originating from Wis 2-1A retrotransposons are much higher in newly synthesized wheat amphiploids (two or more diverged genomes in the same nucleus). On activation, both Wis 2-1A long terminal repeats drive the readout synthesis of new transcripts from adjacent sequences including the antisense or sense strands of known genes. Here we report that activation of these antisense or sense transcripts is associated with silencing or activation of the corresponding genes, respectively. These data, together with the abundance of retrotransposons in genomes and their ability to be activated by various signals, support the view of transposons as potential controlling elements.

TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes.

The Toll/interleukin-1 receptor (TIR) domain is found in one of the two large families of homologues of plant disease resistance proteins (R proteins) in Arabidopsis and other dicotyledonous plants. In addition to these TIR-NBS-LRR (TNL) R proteins, we identified two families of TIR-containing proteins encoded in the Arabidopsis Col-0 genome. The TIR-X (TX) family of proteins lacks both the nucleotide-binding site (NBS) and the leucine rich repeats (LRRs) that are characteristic of the R proteins, while the TIR-NBS (TN) proteins contain much of the NBS, but lack the LRR. In Col-0, the TX family is encoded by 27 genes and three pseudogenes; the TN family is encoded by 20 genes and one pseudogene. Using massively parallel signature sequencing (MPSS), expression was detected at low levels for approximately 85% of the TN-encoding genes. Expression was detected for only approximately 40% of the TX-encoding genes, again at low levels. Physical map data and phylogenetic analysis indicated that multiple genomic duplication events have increased the numbers of TX and TN genes in Arabidopsis. Genes encoding TX, TN and TNL proteins were demonstrated in conifers; TX and TN genes are present in very low numbers in grass genomes. The expression, prevalence, and diversity of TX and TN genes suggests that these genes encode functional proteins rather than resulting from degradation or deletions of TNL genes. These TX and TN proteins could be plant analogues of small TIR-adapter proteins that function in mammalian innate immune responses such as MyD88 and Mal.

Molecular characterization and in silico expression analysis of a chalcone synthase gene family in Sorghum bicolor

Recent use of Sorghum bicolor as a target for grass genomics has presented new resources for gene discovery in novel metabolic pathways in Poaceae. Sorghum synthesizes a unique class of flavonoid phytoalexins, the 3-deoxyanthocyanidins, in response to fungal infection. The biosynthetic pathways for 3-deoxyflavonoids are largely uncharacterized but are known to involve transcriptional activation of chalcone synthase (CHS). CHS, or naringenin CHS, catalyses the formation of naringenin, the precursor for different flavonoids. We have isolated seven sorghum CHS genes, CHS1–7, from a genomic library on high-density filters. CHS1–7 are highly conserved and closely related to the maize C2 and Whp genes. Several of them are also linked in the genome. These findings suggest that they are the result of recent gene duplication events. Expression of the individual CHS genes was studied in silico by examination of expressed sequence tag (EST) data available in the public domain. Our analyses suggested that CHS1–7 were not differentially expressed in the various growth and developmental conditions represented by the cDNA libraries used to generate the EST data. However, we identified a CHS-like gene, CHS8, with significantly higher EST abundance in the pathogen-induced library. CHS8 shows only 81–82% identity to CHS1–7 and forms a distinct subgroup in our phylogenetic analysis. In addition, the active site region contains substitutions that distinguish CHS8 from naringenin CHS. We propose that CHS8 has evolved new enzymatic functions that are involved in the synthesis of defence-related flavonoids, such as the 3-deoxyanthocyanidins, during fungal infection.

Evolutionary dynamics of grass genomes

SummaryThe grass family (Poaceae) has been the subject of intense research over the past decade. Although other angiosperm families contain more species and more genera, the Poaceae exceed all other families in ecological dominance and economic importance. Research has focused on the evolutionary relationships among grasses as well as the structure of grass genomes. Here I examine the evolutionary dynamics of grass genomes in a phylogenetic framework. It is clear that grass genomes are evolutionarily labile for many characteristics, including genome size and chromosome number. Variation in genome size among grasses probably reflects fluctuations in the amount of repetitive DNA per genome, but the history and causes of chromosome number changes remain unclear. Despite substantial variation among genomes, comparative maps suggest that grass genomes retain extensive regions of colinearity. By reanalyzing some comparative map data and also by reviewing comparative sequence data, I argue that the current colinearity paradigm requires reassessment. Contents Summary 15 I. Introduction 16 II. Grass relationships, chromosome numbers and genome size 17 1. Grass relationships 17 2. The timescale of grass evolution 17 3. The evolution of chromosome number 18 4. The evolution of genome size 19 III. Comparative maps and sequencing 21 1. Comparative maps of the grasses 21 2. Limitations of map data for evolutionary analyses 22 3. Synteny among grass genomes: a reanalysis 23 4. Microsynteny: comparative grass sequences 24 IV. Conclusions 25 Acknowledgements 26

Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis

Comparative and Functional Genomics Comp Funct Genom 2002; 3: 165–166. Published online 21 March 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002 / cfg.164 Conference Review Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis Wusirika Ramakrishna 1 *, Jianxin Ma 1 , Phillip SanMiguel 2 , John Emberton 1 , Jorge Dubcovsky 3 , Bryan A Shiloff 4 , Zeyu Jiang 4 , Nils Rostoks 5 , Carlos S Busso 3 , Matthew Ogden 1 , Eric Linton 6 , Andris Kleinhofs 5 , Katrien M Devos 7 , Joachim Messing 6 and Jeffrey L Bennetzen 1 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA Purdue University Genomics Core, S004 WSLR, Purdue University, West Lafayette, IN 47907, USA Department of Agronomy & Range Science, University of California, Davis, 95616 CA, USA National Center for Genome Resources, Santa Fe, NM 87505, USA Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA PGIR-Waksman Institute, Rutgers University, Piscataway, NJ 08855, USA John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK * Correspondence to: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. E-mail: wusirika@purdue.edu Grass genomes show extensive colinearity based on comparative genetic maps, although some large chromosomal rearrangements mark particular lineages. Small rearrangements involving one or a few genes would be missed by these comparative maps. Hence, we have undertaken sequence com- parisons between BACs (bacterial artificial chromo- somes) that contain 80–200 kb genomic segments of several grass species. Rp1 is a complex disease resistance locus in maize that provides race-specific resistance to the leaf rust disease caused by the fungus Puccinia sorghi. Sequence analysis of maize and sorghum Rp1 BACs revealed two Rp1 homologues and twelve other gene-homologous sequences, of which at least ten genes were truncated in one maize segment and eight gene-homologous segments were found in a second maize segment, of which two were Rp1-related and the other six were truncated. The truncated gene segments may have arisen by break repair, probably through homologous or illegitimate recombination. A 43 kb region with an Rp1 homologue, six truncated genes and three Opie retrotransposons was duplicated on two maize BACs. Estimation of divergence times for the Rp1 Copyright # 2002 John Wiley & Sons, Ltd. homologues, the three Opie elements and the inter- vening regions between duplicated regions are consistent with the duplication having occurred within the last 200 000 years. The Retrotransposons Opie-B, Opie-C and Opie-D were inserted before this duplication. In sorghum, the sequenced region includes a cluster of five Rp1 homologues, of which two are truncated with N-terminal deletions. Of the other three Rp1 homologues, a stop codon is present in one and a retrotransposon is inserted in another. The Rp1-homologous region in sorghum has several genes that are either duplicated, inverted, or both. Five duplicated genes other than the Rp1 homologues are present. Physical mapping revealed the presence of eleven Rp1 homologues that mapped to about 400 kb in B73 maize. Six Rp1 homologues mapped to about 50 kb in sorghum inbred BTr623 to a region on linkage group H that is colinear with maize chromosome 10. The Waxy1 gene encodes UDP-glucose starch glycosyl transferase, an enzyme that converts amy- lose to amylopectin. Wx1 is in syntenic locations in all of these grass species, although the maize Wx1 is within a paracentric inversion that places it near centromeric heterochromatin. Sequence analysis of

Gene-Containing Regions of Wheat and the Other Grass Genomes

Deletion line-based high-density physical maps revealed that the wheat (Triticum aestivum) genome is partitioned into gene-rich and -poor compartments. Available deletion lines have bracketed the gene-containing regions to about 10% of the genome. Emerging sequence data suggest that these may further be partitioned into "mini" gene-rich and gene-poor regions. An average of about 10% of each gene-rich region seem to contain genes. Sequence analyses in various species suggest that uneven distribution of genes may be a characteristic of all grasses and perhaps all higher organisms. Comparison of the physical maps with genetic linkage maps showed that recombination in wheat and barley (Hordeum vulgare) is confined to the gene-containing regions. Number of genes, gene density, and the extent of recombination vary greatly among the gene-rich regions. The gene order, relative region size, and recombination are highly conserved within the tribe Triticeae and moderately conserved within the family. Gene-poor regions are composed of retrotransposon-like non-transcribing repeats and pseudogenes. Direct comparisons of orthologous regions indicated that gene density in wheat is about one-half compared with rice (Oryza sativa). Genome size difference between wheat and rice is, therefore, mainly because of amplification of the gene-poor regions. Presence of species-, genera-, and family-specific repeats reveal a repeated invasion of the genomes by different retrotransposons over time. Preferential transposition to adjacent locations and presence of vital genes flanking a gene-rich region may have restricted retrotransposon amplification to gene-poor regions, resulting into tandem blocks of non-transcribing repeats. Insertional inactivation by adjoining retro-elements and selection seem to have played a major role in stabilizing genomes.

Copia-Like Retrotransposons in the Rice Genome: Few and Assorted

We performed a comprehensive analysis of Ty1-copia-like retrotransposons in about 10% of the Oryza sativa genome and identieed 100 elements. These were divided into nine classes by their reverse transcriptase similarity and into 39 families according to the sequences of their long terminal repeats (LTRs). The deduced total number of copia-like elements in rice is 1000, comprising 1.7% of the genome. Solo LTRs and truncated elements comprise an additional 2.3% of the genome. This is low compared with other plants, especially grasses, but comparable to Arabidopsis. However, the total number of families in the genome, at least 50, is similar to that in other plants. At least some of these classes are present in the genomes of other grasses, and related elements can be found in dicotyledonous plants. The transcriptional activity of each family was estimated by searching for homologous expressed sequence tags in databases. No correlation was found between the number of homologous expressed sequence tags and family size. In comparison with the copia retrotransposons, 222 gypsy-like and 66 LINE-like retroelements, as well as eve pararetrovirus-like elements, were found, corresponding to about 2220, 660, and 50, respectively, in the genome. A low rate of retrotransposon transcription and a high rate of loss of integrated copies by ectopic, intrachromosomal recombination are proposed as the reasons for the paucity of retrotransposons in the rice genome.

An integrated physical and genetic map of the rice genome.

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 ( approximately 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.