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,3
ák**
* Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
Genetic Resources Conservation Program, University of California, Davis, California 95616
USDA-ARS Western Regional Research Center, Albany, California 94710-1105
Department of Agronomy, University of Missouri, Columbia, Missouri 65211
¶ USDA-ARS Plant Genetics Research Unit, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
& Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502
** Department of Agronomy and Range Science, University of California, Davis, California 95616
Department of Plant Breeding, Cornell University, Ithaca, New York 14853
Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108
Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170
¶¶ Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105
&& Kyoto University, Kyoto, 606, Japan
*** Department of Botany and Plant Sciences, University of California, Riverside, California 92521
5 Corresponding author: Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164.
E-mail: ksgill{at}wsu.edu
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ABSTRACT |
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100 times larger than the model plant Arabidopsis. Even in Arabidopsis only 45% of the genome represents the gene-containing fraction that is interspersed with noncoding DNA primarily composed of retrotransposon-like repetitive sequences (BARAKAT et al. 1997; BENNETZEN et al. 1998; SIDHU and GILL 2004).
Estimates for the gene-containing fraction of the wheat genome range from 1 to 5% obtained from the available sequence data comparisons with other plant genomes to 15% by DNA reassociation kinetics experiments (FLAVELL et al. 1974; SANDHU and GILL 2002; SIDHU and GILL 2004). Deletion mapping of 2000 gene marker loci showed that genes on wheat chromosomes are also unevenly distributed (GILL et al. 1996a,b; FARIS et al. 2000; SANDHU et al. 2001; SANDHU and GILL 2002; AKHUNOV et al. 2003a,b). About 30% of the wheat genome appears to contain >85% of the genes (ERAYMAN et al. 2004). The remaining 70% of the genome, present as large blocks interspersed by the gene-rich regions, appears to be gene empty. Therefore, targeting the expressed portion of the genome is particularly important for wheat.
Obtaining partial cDNA sequences [expressed sequence tags (ESTs)] from various developmental stages and in response to various biotic and abiotic stresses of the plant is an efficient, economical, and quick approach to target the expressed portion of any genome. About 19 million ESTs representing 600,000 unigenes from >80 organisms are available (http://www.ncbi.nlm.nih.gov; ADAMS et al. 1991). For wheat, >500,000 ESTs corresponding to 22,000 unigenes have been isolated. However, the full potential of the utility of ESTs in genomics cannot be realized without revealing their physical location on chromosomes. Physical mapping of ESTs is particularly important in wheat because of the highly uneven distribution of genes on chromosomes.
Physical mapping of DNA markers is relatively easy in wheat because a wealth of aneuploid stocks is available. A complete series of nullisomic-tetrasomic (NT; a line lacking a pair of chromosomes, loss of which is compensated for by an extra pair of one of its homoeologs) and ditelosomic (DT) lines (SEARS 1954) can be used to reveal arm location of markers (ANDERSON et al. 1992). In addition, 436 chromosome deletion lines are available for the 21 wheat chromosomes that can be used for intrachromosomal mapping (ENDO and GILL 1996). These stocks have been extensively used to physically map >2000 DNA markers (WERNER et al. 1992; GILL et al. 1993; KOTA et al. 1993; HOHMANN et al. 1994; DELANEY et al. 1995a,b; MICKELSON-YOUNG et al. 1995; GILL et al. 1996a,b; FARIS et al. 2000; WENG et al. 2000; SANDHU et al. 2001; DILBIRLIGI et al. 2004; ERAYMAN et al. 2004).
A National Science Foundation-funded collaborative project was initiated with a goal to physically map 10,000 wheat unigene ESTs using the aneuploid and deletion stocks. Wheat homoeologous group 6 data are reported in this article. Similar data for the other six homoeologous groups are presented in the accompanying articles in this issue. We also report identification of rice chromosomal regions homologous to wheat group 6 chromosomes and the use of rice to reveal EST order within each wheat bin.
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MATERIALS AND METHODS |
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EST selection:
As of February 2, 2004, 8318 singletons from 117,000 ESTs derived from 37 cDNA libraries were mapped by the whole project. Details concerning the cDNA libraries, ESTs, and singletons are given elsewhere (http://wheat.pw.usda.gov/NSF; LAZO et al. 2004; ZHANG et al. 2004). For the analysis presented here and in the accompanying articles in this issue, the March 17, 2003, data set of 4485 mapped and verified ESTs was used. From this data set, 882 ESTs mapped to homoeologous group 6.
Deletion mapping:
Genomic DNA isolation, restriction enzyme digestion, and gel-blot analysis were performed as described by SANDHU et al. (2001). Gel-blot analysis was performed using 15 µg of genomic DNA digested with EcoRI enzyme. The NT, DT, and the deletion lines were used in a single hybridization reaction on a set of five filters. The lane order for the filters is provided at http:/wheat.pw.usda.gov/NSF. Each fragment band (locus) was mapped to a chromosome region (bin) flanked by breakpoints of the largest deletion possessing the fragment and the smallest deletion lacking it. The chromosome size data of CS were taken from B. S. GILL et al. (1991). The number of expected loci per arm was calculated on the basis of its physical length. The mapping data along with the gel-blot analysis images are available at http://wheat.pw.usda.gov/cgi-bin/westsql/map_locus.cgi.
Consensus physical map:
A consensus physical map of homoeologous group 6 chromosomes was constructed using the criteria described in GILL et al. (1996a)(b) except that only the ESTs that detected orthologous loci on all three chromosomes were used. The breakpoints of all group 6 deletions were placed on a hypothetical chromosome drawn to scale on the basis of the mean length of group 6 chromosomes. The deletion mapping data from the three chromosomes were then combined to position each EST to the shortest possible chromosome interval. In case of a discrepancy, a location consistent with two homoeologs was used.
Wheat-rice comparisons:
The 882 group 6 ESTs were compared with the rice genomic sequence using "blast" (http://www.ncbi.nih.gov/; ALTSCHUL et al. 1997). A cutoff E-value of E < 10–20 and sequence length >100 bases (for E-values < E < 10–20) were used to identify rice homologs that were equivalent to >65% nucleotide sequence homology. Rice bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) contigs (http://rgp.dna.affrc.go.jp) corresponding to each group 6 bin were identified and used to order 385 group 6 wheat ESTs.
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RESULTS |
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TOPABSTRACTMATERIALS AND METHODSRESULTSDISCUSSIONACKNOWLEDGEMENTSLITERATURE CITED |
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2, P = 0.012) between the observed and the expected numbers (Figure 3). In general, the observed number of loci for the short arms was lower than expected. For example, 46% of the loci were expected to be present on 6BS whereas only 40% were observed. Consequently, the long arm had 11% more loci than expected. Similar observations were made for the other two chromosomes.
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1.6 µm in length and that translates to 106 Mb DNA (B. S. GILL et al. 1991). The calculated EST density based on the 27 loci mapped to the bin was 0.25 loci/Mb. The bin distal to deletion 6DS-6 had the highest density, 16 loci/Mb, with 47 loci and a size of 3 Mb. Similarly, EST density in the 6A bin distal to deletion 6AL-8 was 4.38 loci/Mb compared to 0.63 loci/Mb for the bin proximal to deletion 6AL-4. Detailed mapping information for all the ESTs in each group 6 bin can be accessed from the GrainGenes database website (http://wheat.pw.usda.gov/wEST).
Copy number of expressed sequences:
On average, each EST detected 5.8 fragment bands with a range from 1 to 39. Frequency of loci detected by group 6 ESTs in comparison with other homoeologous groups showed that only 37% of the ESTs detected the expected 3 or 4 fragment bands (Figure 4). About 11% of the ESTs detected only 1–2 loci, suggesting deletion of homoeologous sequences. The remaining 52% of the ESTs detected 5 or more fragment bands. From the total 2849 loci, 2043 mapped to group 6 chromosomes and the remaining 806 mapped on the other chromosomes. Approximately 30% of loci were duplicated. Of these, 6% were intrachromosomal duplications and the remaining were on other chromosomes. Among the 30 intrachromosomal duplications, 15 were on opposite arms. No difference was observed among homoeologs for the rate of intrachromosomal duplications. However, >75% of these duplications were observed in the proximal 50% of the chromosomes. The proximal bins C-6AL4, C-6DS2, and C-6AS1 showed the greatest number of duplications.
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80% of the ESTs (Figure 5). The number of ESTs per bin ranged from zero (in the long-arm bin 0.36-0.40 and the short-arm bin 0.79-Sat) to 49 (in the long-arm bin 0.55-0.68). Because of significant size differences among bins, EST density was calculated per unit size. The EST density per unit chromosome length ranged from 0% in consensus regions 0.36–0.40 of the long arm and 0.79–Satellite (Sat) of the short arm to 23% in the short-arm region Sat–0.99 (Figure 5). In general, the smaller-sized bins had a higher EST density. For example, the short-arm regions Sat–0.99 and 0.99–1.00 (3 Mb each) accounted for 20–23% of the ESTs.
Comparative mapping:
To find rice regions corresponding to each of the group 6 bins, 882 group 6 ESTs were compared against the available rice sequences. At the level of stringency used for comparison, only 385 (43%) of the 882 wheat ESTs identified rice homologs; of these, 225 (58%) showed homology to rice chromosome 2, whereas the remaining 160 (42%) corresponded to regions on the other 11 rice chromosomes. The percentage of the wheat ESTs mapping on the other rice chromosomes ranged from 1.3% on chromosome 11 to 8.3% on chromosome 3. With a mean of 6.5, the number of rice chromosomes represented in each wheat bin ranged from 1 (in the long-arm bin 0.36–0.40) to 11 (in the long-arm bin 0.80–1.00) (Figure 6). Within each wheat bin, rice chromosomes other than chromosome 2 were identified by ESTs ranging from 1 to 6 with an average of 2.7. However, chromosome-specific rice contigs corresponding to each wheat bin were discontinuous as homologs were not present for all BACs/PACs present in rice contigs.
To examine differences among wheat bins for rice homology, the number of ESTs per consensus region (Figure 6, blue bar chart) was compared with that of ESTs showing homology to rice sequence (Figure 6, red bar chart). The width of the blue bar chart was drawn to scale on the basis of the location of 225 ESTs that were present on the consensus physical map. The width of the red bar chart was drawn to scale using 385 ESTs that identified rice homologs. Significant differences were observed among the wheat bins for their homology to rice. For example, wheat regions 0.29–0.36 and 0.55–0.68 on the long arm and 0.76–0.79 on the short arm showed the highest levels of homology with the rice chromosomes (Figure 6). On the other hand, the long-arm regions 0.36–0.40 and 0.68–0.74 and short-arm region 0.79–Sat possessed the least homology. Wheat ESTs mapping on all homoeologs identified rice homologs more frequently than others did. Of the 262 ESTs present on the consensus map, 143 (54%) detected rice homologs compared to 39% for the remaining ESTs.
Rice BAC/PAC contigs corresponding to each of the group 6 bins were used for intrabin ordering of ESTs (Table 1). The order of the 385 wheat ESTs present in the 16 bins of the consensus map was revealed using rice sequences. Of these, 219 were homologous to rice chromosome 2, 32 to chromosome 3, 17 to chromosome 1, and the remaining were homologous to other rice chromosomes.
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DISCUSSION |
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10,000–20,000 gene loci per homoeologous group (SIDHU and GILL 2004). Here we report physical mapping of >2000 loci (10–20% of the total) for wheat homoeologous group 6. We also show the general distribution of genes on the chromosomes. Deletion mapping revealed significant differences among group 6 homoeologs for the number of loci. The comparison between the expected and observed numbers of loci indicated that the number of loci is not always proportional of the size of the chromosome arm. Maximum number was observed for the 6B and minimum for 6D. This difference may partly be due to the variable sizes of the homoeologs, which are predicted to be 863, 673, and 667 Mb for 6B, 6D, and 6A, respectively (B. S. GILL et al. 1991). Another factor explaining this difference may be the number of duplicated loci that may differ among homoeologs.
Dramatic differences were observed for the number of loci per bin. These differences were more pronounced on the consensus physical map mainly because there were three times more breakpoints resulting in a finer resolution. The estimated bin size on the individual deletion maps ranged from 3 (the bin distal to deletion 6DS-6) to 299 Mb (C-6BS-5) with a mean of 88 Mb (Figure 1). On the other hand, consensus-map bin size ranged from 3 (for short-arm bin 0.99–1.00) to 119 Mb (for short-arm bin 0.0–0.35) with a mean of 43 Mb (Figure 5). More than a 30-fold difference was observed for gene density among bins on the consensus map compared to a 14-fold difference in size among individual bins. This comparison suggests that the difference in gene density may be even greater if additional breakpoints were available (GILL et al. 1996b; ERAYMAN et al. 2004). The limitations of the consensus map construction are pointed out by the fact that 15% of the ESTs had discrepant locations among the homoeologs. Although order and colinearity are conserved among the three genomes for most of the genes, significant differences may be present due to differential amplification of the three genomes, chromosomal rearrangements, and gene copy number.
Using only one restriction enzyme, 30% of the ESTs detected loci on all three chromosomes, 22% detected loci on two, and the remaining ESTs detected loci only on one of the three homoeologs. This large number of ESTs mapping to only one of the chromosomes can be attributed to the use of only one restriction enzyme. By using two restriction enzymes for a similar physical mapping experiment, 81% (61/75) wheat group 1 gene markers detected loci on all three homoeologs, 12% (9/75) detected loci on two, and only 7% (5/75) detected loci on one of the three genomes (SANDHU et al. 2001). In the present study, 45% (2305/5154) of the fragments detected by group 6-specific ESTs were monomorphic and that may be resolved with the use of additional restriction enzymes.
The extent and distribution of EST duplication on group 6 chromosomes was similar to that reported for the wheat genome as a whole (QI et al. 2004). About 21% of the wheat sequences have paralogous loci (AKHUNOV et al. 2003a). In this study, 32% (287) of the ESTs detected paralogous loci on other chromosomes ranging from 13% for group 4 to 20% for groups 2 and 7. About 4% of the ESTs detected paralogous loci on group 6, of which one-half were on the same chromosome. In barley, 20–30% of probes detected duplicated loci (GRANER et al. 1991; KLEINHOFS et al. 1993). Some of the other similar estimates obtained from the genetic linkage analysis were 28% of the cDNA clones and 34% of the PstI genomic clones in T. monococcum L. (DUBCOVSKY et al. 1996), and 31% in Aegilops tauschii Coss. (K. S. GILL et al. 1991). These duplicated loci could have resulted from interchromosomal exchanges, intergenomic invasions, and dispersion of specific DNA elements during genome evolution through polyploidization (WENDEL 2000; AKHUNOV et al. 2003a).
Several wheat-rice comparisons have been made and slightly different results were observed, depending on methods and criteria. Genetic linkage-map comparisons between wheat and rice identified syntenic chromosomes between the two genomes (AHN et al. 1993; KURATA et al. 1994; DEVOS et al. 1995; SHERMAN et al. 1995; VAN DEYNZE et al. 1995; SAGHAI-MAROOF et al. 1996; DEVOS and GALE 1997). Depending upon stringency, sequence comparisons between wheat and rice showed that 50–98% of the rice genes are similar to those of wheat. For example, GOFF et al. (2002) reported 98% protein sequence homology among rice, maize, wheat, and barley. On the other hand, 65% of wheat ESTs identified rice homologs at E < 10–15 (SORRELLS et al. 2003). Similar comparisons in the present study at a slightly higher stringency showed that only 43% of group 6 ESTs have rice homologs. Even at a liberal cutoff value (E < 10–1), only 67% (593/882) of the ESTs detected rice homologs. Therefore, we conclude that at least 33% of the wheat ESTs do not have rice homologs.
Previous studies using RFLP markers (GALE and DEVOS 1998) and wheat ESTs (SORRELLS et al. 2003) have reported that wheat homoeologous group 6 chromosomes illustrate substantial homology to rice with the best conservation of gene order and content with rice chromosome 2 (SORRELLS et al. 2003). In the present study, however, of the 43% group 6 ESTs that identified rice homologs, only 58% were on rice chromosome 2. The remaining were present as small blocks on the other rice chromosomes.
Individual bin comparisons with rice sequences showed that, in addition to chromosome 2, other rice chromosome segments were present in all the bins as 1–10 blocks of varying sizes. Each rice chromosomal block was identified by 1–6 wheat ESTs, suggesting that these blocks are not paralogous loci but are true homologs of wheat group 6 scattered on other rice chromosomes (Figure 6). Since most of the rice chromosomal blocks homologous to wheat group 6 bins have been identified, it should be possible to use the rice sequence information efficiently and accurately for wheat genomics. Furthermore, rice BAC/PAC contigs can be used to order wheat ESTs within bins. In this study, we resolved the order of 385 wheat ESTs within 16 bins (Table 1). However, the accuracy of this order needs to be determined.
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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: USDA-ARS Biosciences Research Laboratory, Fargo, ND 58105-5674.
4 Present address: Plant Breeding and Acclimatization Institute, Radzikow 05-870 Blonie, Poland.
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  J. Salse, S. Bolot, M. Throude, V. Jouffe, B. Piegu, U. M. Quraishi, T. Calcagno, R. Cooke, M. Delseny, and C. Feuillet Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution PLANT CELL, January 1, 2008; 20(1): 11 - 24. [Abstract] [Full Text] [PDF]
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 J. King, I. P. Armstead, S. I. Donnison, L. A. Roberts, J. A. Harper, K. Skot, K. Elborough, and I. P. King Comparative Analyses Between Lolium/Festuca Introgression Lines and Rice Reveal the Major Fraction of Functionally Annotated Gene Models Is Located in Recombination-Poor/Very Recombination-Poor Regions of the Genome Genetics, September 1, 2007; 177(1): 597 - 606. [Abstract] [Full Text] [PDF]
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S. Cho, D. F. Garvin, and G. J. Muehlbauer Transcriptome Analysis and Physical Mapping of Barley Genes in Wheat-Barley Chromosome Addition Lines Genetics, February 1, 2006; 172(2): 1277 - 1285. [Abstract] [Full Text] [PDF]
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G. R. Lazo, S. Chao, D. D. Hummel, H. Edwards, C. C. Crossman, N. Lui, D. E. Matthews, V. L. Carollo, D. L. Hane, F. M. You, et al. Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.): EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map Genetics, October 1, 2004; 168(2): 585 - 593. [Abstract] [Full Text] [PDF]
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D. Zhang, D. W. Choi, S. Wanamaker, R. D. Fenton, A. Chin, M. Malatrasi, Y. Turuspekov, H. Walia, E. D. Akhunov, P. Kianian, et al. Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.) Genetics, October 1, 2004; 168(2): 595 - 608. [Abstract] [Full Text] [PDF]
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Miftahudin, K. Ross, X.-F. Ma, A. A. Mahmoud, J. Layton, M. A. R. Milla, T. Chikmawati, J. Ramalingam, O. Feril, M. S. Pathan, et al. Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4 Genetics, October 1, 2004; 168(2): 651 - 663. [Abstract] [Full Text] [PDF]
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L. L. Qi, B. Echalier, S. Chao, G. R. Lazo, G. E. Butler, O. D. Anderson, E. D. Akhunov, J. Dvorak, A. M. Linkiewicz, A. Ratnasiri, et al. A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat Genetics, October 1, 2004; 168(2): 701 - 712. [Abstract] [Full Text] [PDF]
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