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,1
ák,3
* Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170
U.S. Department of Agriculture (USDA)-Agricultural Research Service (ARS), Western Regional Research Center, Albany, California 94710-1105
USDA-ARS Plant Genetics Research Unit, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
Genetic Resources Conservation Program, University of California, Davis, California 95616
¶ Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502
& Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
** Department of Plant Breeding, Cornell University, Ithaca, New York 14853
Department of Agronomy and Range Science, University of California, Davis, California 95616
Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105
Department of Agronomy, University of Missouri, Columbia, Missouri 65211
¶¶ Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108
4 Corresponding author: Department of Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170.
E-mail: nlapitan{at}lamar.colostate.edu
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ABSTRACT |
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e–10), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses.
The genome size of hexaploid wheat is the largest (16,979 Mbp) among all cereal crops, including oat (Avena sativa L.; 12,961 Mbp), maize (Zea mays L.; 2671 Mbp), sorghum (Sorghum bicolor L.; 735–1642 Mbp), and rice (Oryza sativa L; 490 Mbp; BENNETT and LEITCH 2003). The hexaploid wheat genome is also much larger than any of the current plant model species, 
35 times larger than rice and 99 times larger than Arabidopsis thaliana (172 Mbp) (BENNETT and LEITCH 2003).
In any genome-sequencing project, the central goal is the discovery of all the genes in the target organism and the establishment of their chromosomal location (BENNETZEN 2002). The completion of genome sequencing in rice (GOFF et al. 2002; YU et al. 2002; http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/irgsp-status.cgi, http://www.gramene.org/) and Arabidopsis (ARABIDOPSIS GENOME INITIATIVE 2000) opened the door to comparative plant genomics or comparative plant biology. Because of the large size of the hexaploid wheat genome, complete sequencing has not been feasible. Large-scale discovery and isolation of genes and deciphering of gene function in wheat and its relatives must rely on other, less direct methods.
An EST is a segment of a sequence from a cDNA clone complementary to an mRNA sequence. Thus ESTs are segments of expressed genes (ADAMS et al. 1991). The ESTs (mRNAs 
cDNAs) can be isolated from multiple tissues under various treatments and used to identify as many genes as possible in an organism. The EST approach facilitates the tagging of genes in a relatively short time at a fraction of the cost of complete genome sequencing, provides new genetic markers, and serves as a resource in diverse biological research fields (ADAMS et al. 1991). This approach has provided a new resource for the analysis of chromosome sequences and gene discovery in many organisms, such as Homo sapiens (ADAMS et al. 1991, 1995; HILLIER et al. 1996), Mus musculus (MARRA et al. 1999), Rattus norvegicus (SCHEETZ et al. 2001), Danio rerio (CLARK et al. 2001), Medicago truncatula (COVITZ et al. 1998), maize (FERNANDES et al. 2002), and rice (EWING et al. 1999). Developing ESTs has become a top priority for crop genomics worldwide (BRIGGS 1998). Development and deletion mapping analysis of ESTs from hexaploid wheat were conceived by a group of U. S. researchers as a cost-effective approach and a short cut to gene discovery, comparative genomics, and evolutionary genomics.
Hexaploid wheat has seven homoeologous groups of chromosomes, each containing one A, B, and D chromosome from each one of the donor genomes (SEARS 1969). The group 1 homoeologous chromosomes are the most studied and understood of the wheat chromosome groups, primarily because they house major clusters of agronomically important genes. The group 1 and the group 2 chromosomes have 100 each of the 615 genes of known chromosomal location, more than any of the other groups (MCINTOSH et al. 2003). There are clusters of resistance genes in wheat chromosome 1B, including at least 22 genes and QTL conferring resistance (PENG 2000; DILBIRLIGI et al. 2004). Numerous genes and gene families expressed during seed development are located in group 1, such as high-molecular-weight glutenins, low-molecular-weight glutenins, 
- and 
-gliadins, the triplet protein, and several seed-specific globulins (DUBCOVSKY et al. 1997). Among seven domestication syndrome factors detected in wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.], two were located on chromosome 1B (PENG et al. 2003). In a single gene-rich region, the 1S0.8 region of the short arm of chromosome 1 in Triticeae, as many as 75 genes were identified (SANDHU et al. 2001).
The goal of the U.S. wheat EST project was to establish the chromosomal location of genes in the hexaploid wheat genomes. ESTs representing wheat unigenes were physically mapped to individual chromosomes/chromosomal intervals using wheat nullisomic-tetrasomic and ditelosomic lines (SEARS 1966) and deletion stocks (ENDO 1988, 1990; ENDO and GILL 1996). This article summarizes the EST mapping results for group 1 chromosomes of hexaploid wheat. Patterns of distribution and duplication of ESTs within and among the group 1 chromosomes of wheat and comparisons with rice and Arabidopsis genome sequences are discussed.
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MATERIALS AND METHODS |
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TOPABSTRACTMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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Plant materials:
Hexaploid wheat has an extensive collection of aneuploid and deletion stocks in the Chinese Spring background that are ideal for chromosome mapping, allowing for virtually every DNA marker to be assigned to a specific chromosome/arm/interval without requiring intragenomic polymorphism (SEARS 1954, 1966; SEARS and SEARS 1978; ENDO 1988, 1990; ENDO and GILL 1996). A total of 146 cytogenetic stocks including 21 nullisomic-tetrasomic, 24 ditelosomic, and 101 deletion lines were used. The genetic stocks for EST mapping were provided by the Wheat Genetics Resource Center, Kansas State University, and cytologically and/or molecularly verified by all 10 mapping laboratories (http://wheat.pw.usda.gov/NSF; QI et al. 2003, 2004). DNA samples were isolated following protocols established in the individual laboratories.
Southern hybridization:
The conventional Southern hybridization approach was adopted with some minor modifications (http://wheat.pw.usda.gov/NSF/project/mapping_data.html). About 20 µg of genomic DNA were digested with EcoRI enzyme. A mixture of digested products of 
DNA using HindIII and BstEII was used as the size ladder. The digested DNA samples were separated on a 1.0% agarose gel and blotted onto a Hybond N+ membrane (Amersham Biosciences, Buckinghamshire, UK). A set consisting of five Southern blots, each with 30 lanes (a size ladder was included for the first four blots), was hybridized with a single EST clone in each hybridization reaction. More details about Southern hybridization were described by LAZO et al. (2004) and QI et al. (2004).
Localization of ESTs:
Bread wheat is a hexaploid, and the allocation of homoeologous loci to specific chromosomes within a homoeologous group is based on interchromosomal polymorphism. According to presence or absence of the restriction fragments in a given set of DNA lanes of a Southern blot, EST loci were assigned to a specific chromosome, an arm, and/or a deletion bin (SEARS 1954 1966; ENDO 1988, 1990; ENDO and GILL 1996). The EST loci were localized to individual bins in the homoeologous group 1 chromosomes as described by AKHUNOV et al. (2003) and QI et al. (2003)(2004). Southern images were scored by at least two persons in each laboratory, and the edited images and mapping data were uploaded to the project website http://wheat.pw.usda.gov/NSF/project/. Each set of mapping data was further validated by corresponding coordinators of the seven homoeologous chromosome groups at the project website http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus_rev.cgi.
Data analysis:
Only mapping data validated by three persons (http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus_rev.cgi) were used for analyses. Mapping data were reverified by checking all the online images in the project database prior to the analyses. Any ambiguous data were excluded in the analyses. On the basis of the physical size (in micrometers) of chromosomes and chromosome arms (GILL et al. 1991) and the relative length of chromosome deletion bins (ENDO and GILL 1996), the expected number of ESTs/EST loci was estimated under the assumption of random distribution among and along chromosomes. But the expected numbers of ESTs/EST loci in 1A, 1B, and 1D were estimated on the basis of a hypothetical 1:1:1 distribution. EST densities were calculated as the ratio of observed vs. expected ESTs/EST loci for the individual chromosomes, chromosome arms, and chromosome bins. The 
2 test was used to test for independence of distribution patterns of ESTs among and along chromosomes. Loci numbers and distributions of duplicated ESTs across the other six chromosome groups were also analyzed.
The method of constructing the consensus map was as described by GILL et al. (1996a)(b). ESTs that were not mapped to specific bins or fell into two conflicting bins were assigned to consensus chromosome 1, to one chromosome arm, or to a larger combined bin encompassing the two conflicting bins.
To analyze the similarity of wheat consensus chromosome 1 with rice and Arabidopsis sequences, blastN searches of the ESTs—mapped to all three group 1 chromosomes and used to construct the consensus chromosome bin map against rice (http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/irgsp-status.cgi) and Arabidopsis (http://www.arabidopsis.org/) sequence databases—were conducted. E e–10 was adopted as the standard to claim a significant match. BlastX was also used to retrieve the gene function of wheat chromosome 1 ESTs that matched to Arabidopsis. The binomial test was used to detect colinearity of consensus bins with rice chromosomes as described by LINKIEWICZ et al. (2004). A putative orthologous genetic map for each interval, significantly colinear with rice chromosomes 5 and/or 10, of wheat consensus chromosome 1 ESTs was constructed on the basis of the order and position of the corresponding P1-derived artificial chromosome (PAC)/bacterial artificial chromosome (BAC) clones in rice chromosomes 5 and 10. Details of wheat consensus chromosome 1 ESTs and the significantly matched PAC/BAC clones in rice chromosomes 5 and 10 can be retrieved as supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/.
An anomaly was defined as an EST having loci mapped to nonoverlapping bins on homoeologous chromosomes (MUNKVOLD et al. 2004). Mapping data and images of all the EST probes assigned to group 1 chromosomes were examined for such anomalies.
Types of EST duplications analyzed:
Two types of duplications were distinguished, intrachromosome and interchromosome duplications. An intrachromosome duplication is inferred to have occurred when an EST generates two or more loci in one chromosome. The number of intrachromosome duplications was estimated from the difference between the number of loci and the number of EST probes mapped in a particular chromosome. An interchromosome duplication refers to the situation in which an EST maps to chromosomes other than the three homoeologous group 1 chromosomes (1A, 1B, 1D). In testing the observed number vs. the expected number of duplications, we assumed that duplications in other locations occurred randomly, so that the greater the length of a chromosome or bin, the greater the chance of a duplication occurring in that region. The expected number of duplications was therefore determined on the basis of the size of the chromosome or chromosome bin.
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RESULTS |
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2 test showed that deviation from the expected values based on a hypothetical ratio of 1:1:1 (even distribution) was highly significant (P < 0.01) for EST loci, but not significant for EST probes. Thus, it appeared that the mapped EST probes were randomly distributed among the three chromosomes, but the mapped EST loci were not. Chromosome 1B had a larger number and 1A had a smaller number than expected (Table 1). As done by LINKIEWICZ et al. (2004) for homoeologous group 5, the previous analysis was repeated using the subset of EST probes for which all bands were mapped (326 ESTs). Again the 1B chromosome had the largest proportion of probes (265) and loci (317). However, the numbers of EST probes and loci did not significantly deviate from the expected values based on random distribution (Table 1). It seems that this subset of mapped EST probes was randomly distributed among the three group 1 chromosomes.
Distribution pattern of EST loci on the chromosome arms:
Of the 2212 EST loci (Table 1), 2076 were mapped to specific chromosome arms (Table 2) and the other 136 were mapped only to chromosomes or centromere bins. The numbers of EST loci mapped to the long arms of each of the three chromosomes were larger than those mapped to the short arms (Table 2). In comparison with the expected values based on arm length (GILL et al. 1991), the ESTs were randomly distributed between long and short arms for 1A (P = 0.27), nearly randomly for 1B (P = 0.06), and nonrandomly for 1D (P = 0.02) with more observed in the long arm and less than expected in the short arm (Table 2).
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EST density:
EST density is the ratio of the number of mapped ESTs to the expected value based on the length of chromosome/arm/interval. Chromosome 1D had relatively high EST density values, both when all ESTs were used (1.22) and when only the subset for which all loci were mapped was used (1.24); chromosome 1A had the lowest EST density with values 0.84 and 0.88; and chromosome 1B was in between with values of 0.94 and 0.99 (Table 1). The short arms had slightly higher EST densities (>1) than the long arms (<1) for 1A and 1B, but the reverse was true for 1D where the long arm had a higher EST density (>1) than did the short arm (<1; Table 2).
Most of the intervals with EST density <1.0 were in proximal regions near the centromeres. Five intervals were EST rich, having high-EST density: 1AS-0.86-1.00 (3.70), 1BL-0.47-0.69 (1.78), 1DS-0.70-1.00 (1.91), 1DL-0.41-1.00 (1.44), and the 1BS satellite region (3.50; Figure 1). In the consensus chromosome bin map, the EST-rich regions in the short arm were located in the intervals 1S-0.47-0.48 (10.00), 1S-0.84-0.86 (2.50), and 1S-0.86-1.00, including the satellite region (4.13). The EST-rich regions in the long arm were all located in the middle intervals 1L-0.41-0.47 (2.15), 1L-0.47-0.61 (2.00), and 1L-0.61-0.69 (2.00; Figure 1).
Duplications of group 1 ESTs:
EST intrachromosome duplications were not randomly distributed among the three chromosomes with 50% of the duplications occurring in 1B (Table 1). Approximately 13% of the mapped EST unigenes contained at least one EcoRI restriction site, not including sites within introns (MUNKVOLD et al. 2004). Because internal EcoRI sites within the region of hybridization can create duplicated fragments within a bin, the rate of intrachromosome duplications might be overestimated in the present study. However, the multiple EcoRI restriction sites within ESTs would not affect the rates of interchromosome and intergenome duplications.
About 35% (335) of the ESTs mapped to group 1 chromosomes also had loci in one or more of the six other homoeologous groups (Table 3). The 2 test showed that deviation of the observed number of ESTs with duplications in other homoeologous groups from the expected number based on chromosome size was not significant, although group 2 had a relatively large number. It seems that none of the six homoeologous chromosome groups had a significantly closer homoeology with group 1 chromosomes.
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2 = 24.9, P < 0.01), with a larger number than expected in 1B and a smaller number than expected in 1A and 1D. A similar result was observed for distribution of EST duplications along chromosome arms with clustering in the distal bins. In comparison with the expected number derived from chromosome size, deviations of EST duplication in the six other homoeologous groups for all three group 1 chromosomes were not significant.
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e–10) matches with Arabidopsis sequences (Table 5). Of these, 27 (77%) were located on the long arm of wheat consensus chromosome 1 and the other 8 (23%) were on the short arm. These 35 that significantly matched wheat chromosome 1 ESTs were not randomly distributed (P < 0.05) among the five Arabidopsis chromosomes, with an apparently larger number located to chromosome 3 (37%) and fewer to chromosome 1 (11%). Therefore, homoeology of wheat consensus chromosome 1 (W1) ESTs with Arabidopsis was not high (<10%), and the relatively greatest homoeology exists with Arabidopsis chromosome 3.
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e–10) matches to rice sequences (Table 6). All but two of these were associated with specific rice chromosomes. Wheat group 1 ESTs that significantly matched to rice sequences were unevenly distributed (P < 0.01) among the 12 rice chromosomes with 49, 20, and 1–5% located on chromosome 5, chromosome 10, and the other 10 chromosomes, respectively. Therefore, the wheat group 1 ESTs analyzed have high homoeology (75%) with rice, especially rice chromosomes 5 and 10.
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Putative EST order in wheat consensus chromosome 1 based on rice sequences:
Due to the high homoeology with wheat group 1 chromosomes, sequence orders of rice chromosomes R5 and R10 (http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/irgsp-status.cgi) were used to construct an orthologous genetic consensus EST bin map of W1 as shown in Figure 2. Details of this orthologous genetic map are also presented as supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/.
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A total of 53 W1 ESTs significantly matched to 37 R10 BAC/PAC clones spanning a genetic distance of 77.0 cM. About one-third (12) of the R10 sequences matched to two or more W1 ESTs in the proximal regions of the long arm of W1. Of the 37 R10 sequences, 33 matched to W1 ESTs on the long arm. Of the four exceptions, two were duplicated and two were specific to the short arm of W1 (Figure 2).
R5 sequence-matched ESTs apparently predominated over R10 sequence-matched ESTs for the bins with fraction length (FL) > 0.47 in both short and long arms of W1, the reverse was true for the bins with FL < 0.47 in the long arm of W1. There were five intervals without significant colinearity with R5 or R10, and four of them were in the short arm (C-1S-0.47, 1S-0.48-0.50, 1S-0.59-0.70, and 1S-0.70-0.84) of W1. Thus, either these five intervals have no similarity to R5 and R10 sequences or the similarity could not be detected with the existing data.
Anomaly:
An anomaly refers to nonoverlapping map positions for an EST in the chromosome bin maps of the homoeologues. Of the 944 EST probes mapped to group 1 chromosomes, 26 (2.8%) detected anomalies, as defined by MUNKVOLD et al. (2004), involving all three group 1 chromosomes and arms. The distribution of these anomalies among the three group 1 chromosomes is shown in Figure 3. For example, EST BE500081 in the bin C-1BL-0.32 was not mapped to the near-centromere bin on the long arm of either 1A or 1D, but it did map to bin 1AS-0.47-0.86 on 1AS. A total of 13 anomalies were present among 18 of 21 noncentromere bins, and 4, 5, and 4 anomalies were present for 1A, 1B, and 1D chromosomes, respectively. But only 7 of the 13 anomalies were detected by two or more ESTs.
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DISCUSSION |
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TOPABSTRACTMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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100 publications. With the results reported here, 2212 loci, and the previous 1500, >3700 loci have been identified for this group, making it particularly rich in DNA marker loci.
Gene-rich regions in wheat group 1 chromosomes:
It is well established from this study and others that polymorphic DNA markers are not evenly distributed along the chromosomes in both genetic (DEVEY and HART 1993; DUBCOVSKY et al. 1995; GALE et al. 1995; VAN DEYNZE et al. 1995; CADALEN et al. 1997; PENG 2000; PENG et al. 2000) and physical maps (DELANEY et al. 1995a,b; GILL et al. 1996a,b; FARIS et al. 2000; MA et al. 2001). GILL et al. (1996b) identified the 1S0.8 consensus region as gene rich. SANDHU et al. (2001) localized 75 useful genes into this region. We mapped >100 EST loci in regions of similar size in this study on each short arm of the group 1 chromosomes, accounting for >50% of those on the short arm for each chromosome. The short arm region of similar size in the wheat consensus chromosome 1 (16% of the arm) contained 67 ESTs (64.4% of the total in the consensus short-arm map; Figure 1; supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/).
The distribution of ESTs can reveal the approximate expressed gene distribution patterns. We found that ESTs clustered in a few regions in the three group 1 chromosomes (Figure 1). It has been shown that centromeric/proximal regions are relatively gene poor and distal/telomeric regions on the short arms are gene rich (GILL et al. 1996a,b; FARIS et al. 2000). Our results further showed that the telomeric regions on the long arms had a lower gene density than the middle portion of the arms, which contained EST-rich regions/clusters. There are ESTs in the distal bins, but they are located in the proximal regions of those bins and are not at the ends of the chromosomes. The consensus map with a higher number of long-arm bins than the individual chromosomes clearly points this out (Figure 1).
We found that the number of ESTs mapped to the proximal parts of chromosome arms was significantly lower than that mapped to the distal parts (Figure 1). Comparisons of genetic linkage maps and physical maps have indicated that recombination is dramatically reduced in the centromeric regions of grass chromosomes. This recombination reduction is explained as the result of suppression around the centromere or by the centromere itself (DVOáK and CHEN 1984; LUKASZEWSKI and CURTIS 1993; VAN DEYNZE et al. 1995). As shown by AKHUNOV et al. (2003), EST density was positively related with recombination rate (i.e., EST-rich regions have high recombination rates). But the reason for recombination reduction near the centromere may be the low EST (gene) density, rather than centromere suppression.
Duplication of wheat group 1 ESTs:
If an EST probe had loci mapping to more than one chromosome in a genome, then those loci were considered duplicated (AKHUNOV et al. 2003). ANDERSON et al. (1992) reported that 40 of 210 DNA probes hybridized to fragments in more than one homoeologous group and that group 1 chromosomes were involved in the majority of these duplications. VAN DEYNZE et al. (1995) found that many loci were duplicated between group 1 and group 7 chromosomes. DUBCOVSKY et al. (1996) pointed out that 30% of the loci mapped in T. monococcum were duplicated in other chromosomes. AKHUNOV et al. (2003) found that 21% of 730 ESTs had duplicated loci. In the present study, 335 (35%) of 944 ESTs analyzed were mapped to group 1 and at least one of the other six homoeologous groups. The number of group 1 duplications shared by each of the other six homoeologous groups ranged from 113 to 158 ESTs (Table 3). The EST duplication rate in this article seemed much higher than that found by AKHUNOV et al. (2003), and the difference may be derived from the data source (group 1, studied here, vs. all groups studied by AKHUNOV et al. 2003). Duplications of group 1 ESTs were randomly distributed among the other six homoeologous groups, but unevenly distributed among the three group 1 chromosomes with a larger number in 1B and a smaller number in 1A and 1D than expected and, along the chromosome arms, with a larger number in the distal and a smaller number in the proximal regions except 1AL and 1BL (Table 4). These results confirm the conclusion of AKHUNOV et al. (2003) who studied a smaller sample of the ESTs mapped in this project. The high rate of interchromosome duplication of ESTs also confirms that homoology exists among the seven groups of homoeologous chromosomes of wheat.
Anomalies in group 1 chromosomes:
The rate of anomalies was much lower in group 1 than in group 3 (MUNKVOLD et al. 2004). Anomalies may result from biological events such as chromosomal rearrangements, transposition, and gene duplication or be an artifact of technical errors. An anomaly evidenced by a single EST (6 of 13 for group 1 chromosomes) is questionable and likely due to a technical error. However, anomalies involving two or more mapped ESTs with the same location pattern (7 of 13) are more likely to result from a biological event. Of the 7 multi-EST anomalies, three (B, J, and M, Figure 3) were supported by four to five ESTs. These three striking anomalies belong to an intra-arm anomaly, i.e., long (or short) arm to long (or short) arm of two homoeoleogous chromosomes. The chromosome bins involved had different EST densities (Figure 3). These anomalies could have resulted from chromosomal rearrangements, possibly resulting from transposition and gene duplication mainly between chromosome intervals with different gene density.
Homoeologous relationship between wheat consensus chromosome 1 and the rice genome:
Homoeology between wheat and rice genomes was first studied by AHN et al. (1993) and followed by KURATA et al. (1994) and VAN DEYNZE et al. (1995) at the macro level. Recently, SORRELLS et al. (2003), studying a subset of project EST loci involving all homoeologous groups, compared rice and wheat genomes at the DNA sequence level. All studies indicated that rice chromosomes 5 and 10 were homoeologous with group 1 chromosomes of wheat. SORRELLS et al. (2003) also showed that 81% of the rice BAC/PAC clones were matched by wheat ESTs. Our results (Figure 2; Table 6; supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/) further corroborated the close syntenic or homoeologous relationship of wheat consensus chromosome 1 with rice chromosomes 5 and 10.
Comparative mapping based on cDNA clones indicated that rice chromosome 5 was largely conserved with wheat consensus chromosome 1 and that rice chromosome 10 was conserved with a portion of the long arm of wheat consensus chromosome 1. Our results, based on sequence comparison between wheat consensus chromosome 1 ESTs and rice BAC/PAC clones, further identified specific wheat consensus chromosome 1 bins with significant colinearity to rice chromosomes 5 and 10 (Figure 2; Table 6). Since distal segments of wheat chromosomes are gene-rich and recombination-rich regions (DELANEY 1995a,b; GILL et al. 1996a,b; FARIS et al. 2000), we may expect rice chromosome 5 to have close relationships to the gene clusters in the distal regions of wheat consensus chromosome 1. Rice chromosomes 5 and 10 and wheat chromosome 1 were probably differentiated by a chromosome fission/fusion after evolutionary divergence (AHN et al. 1993). As shown in Figure 1, both the EST number and EST density in the C-1L-0.47 region significantly (P < 0.01) exceeded those in the C-1S-0.47 region of wheat consensus chromosome 1. Therefore, we also speculate that, in the process of divergence, the DNA segments corresponding to the current rice chromosome 10 might have been translocated to the proximal region of the long arm of rice chromosome 5. Because of this possible "translocation," the proximal part of the long arm of wheat chromosome 1 is not as gene poor as the counterpart of the short arm appears (Figures 1 and 2).
KURATA et al. (1994) provided evidence for the conservation of gene order between rice and wheat; i.e., many wheat chromosomes contain genes and genomic DNA fragments in a similar order to that found on rice chromosomes. VAN DEYNZE et al. (1995) pointed out that although wheat orthologous loci span all of rice chromosome 5 and 10 linkage maps, loci from the distal portion of the linkage maps for the short arms of the Triticeae chromosomes are not represented in these rice chromosomes. The only two loci from the distal short arm of the linkage maps of the Triticeae that could be detected in rice did not map to homoeologous positions in rice chromosome 5. The linear organizations of genes in nine different genomes of grasses, including wheat, can be described in terms of only 25 "rice linkage blocks" based on genetic mapping using common DNA probes (GALE and DEVOS 1998). Our results, based on DNA sequence comparison and chromosome deletion bin mapping, corroborate, to some extent, the conservation of gene orders between rice and wheat. However, a number of genes not showing any colinearity were also identified. This noncolinearity may be due to chromosome structural changes, gene inversions, transposon-like movements, and inclusion of multi-copy probes. The ESTs in the orthologous regions of wheat consensus chromosome 1 may be ordered following the sequence (BAC/PAC clone) order in rice chromosome 5 or 10, as shown in Figure 2 and supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/. The order of orthologous EST loci in the individual wheat consensus chromosome 1 deletion bins needs to be verified by genetic mapping or complete sequencing of the bins.
It is clear that the three chromosomes of homoeologous group 1 are not perfectly conserved. They are different in physical size and structure (GILL et al. 1991), the extent of polymorphism detected by both molecular markers (PENG et al. 2000) and QTL analysis (PENG et al. 2003), and gene content, density, and duplication (Table 1). Therefore, even though the consensus chromosome 1 is of considerable value in obtaining a general profile of EST distribution patterns of wheat group 1 chromosomes and their colinearity with rice chromosomes 5 and 10, there are limitations to its resolution and validity.
Homoeologous relationship of wheat consensus chromosome 1 with the Arabidopsis genome:
Arabidopsis is the first plant with a completely sequenced genome (ARABIDOPSIS GENOME INITIATIVE 2000). A. thaliana was estimated to contain 25,000 genes, but its genome is 99 times smaller than that of hexaploid wheat (BENNETT and LEITCH 2003). It would be greatly helpful for wheat genomics studies if Arabidopsis information could be transferable to wheat. Initial observations indicated that synteny might be extrapolated to monocot and dicot species (PATERSON et al. 1996). Attempts to establish colinearity between the rice and Arabidopsis genomes suggest that colinearity cannot be detected in comparative genetic mapping studies (DEVOS et al. 1999). In the present study, only 35 (9.5%) of wheat homoeologous group 1 ESTs showed significant matches to the Arabidopsis genome sequences. No significant conservation of gene order was detected between wheat consensus chromosome 1 and Arabidopsis chromosomes (data not shown) with this small number of ESTs. These 35 ESTs represent <30 types of gene function (Table 5). The number of conserved genes shared by monocotyledonous and dicotyledonous plant species seems small. Therefore the DNA sequence data of Arabidopsis do not appear to be very useful in the study of genome organization of wheat or other grass species.
Arabidopsis chromosome 3 accounted for 13 (37.4%) of the DNA segments with significant matches to wheat group 1 ESTs and seems to have the closest relationship, among the five Arabidopsis chromosomes, with wheat consensus chromosome 1 (Table 5). Five (38.5%) of these 13 segments spanning 20.5 Mbp (2.6–23.1 Mbp) of Arabidopsis chromosome 3 corresponded to the ESTs located in the 1L-0.47-0.61 region of wheat consensus chromosome 1 (data not shown). However, as observed between rice and Arabidopsis (DEVOS et al. 1999), there is poor colinearity between wheat consensus chromosome 1 and Arabidopsis chromosome 3.
Interestingly, only 5 (14.3%) of the 35 group 1 ESTs with matches to Arabidopsis were located in the terminal regions of wheat consensus chromosome 1. The common genes shared by wheat consensus chromosome 1 and Arabidopsis appear located in the middle parts of the chromosome arms or the proximal region of the long arm (Table 5).
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ACKNOWLEDGEMENTS |
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FOOTNOTES |
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2 Present address: Department of Agronomy, Iowa State University, Ames, IA 50014-8122.
3 Present address: Plant Breeding and Acclimatization Institute, Radzikow 05-870 Blonie, Poland.
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LITERATURE CITED |
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TOPABSTRACTMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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