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Zhong GY, McGuire PE, Qualset CO, Dvorák J. Cytological and molecular characterization of a Triticum aestivum x Lophopyrum ponticum backcross derivative resistant to barley yellow dwarf. Genome 2012; 37:876-81. [PMID: 18470130 DOI: 10.1139/g94-124] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Barley yellow dwarf is the most damaging virus-caused disease in bread wheat (Triticum aestivum L.). A resistant line, SW335.1.2-13-11-1-5 (2n = 47), derived from a cross of T. aestivum x Lophopyrum ponticum was characterized by meiotic chromosome pairing, by in situ DNA hybridization and by expression of molecular markers to determine its chromosome constitution. All progeny of this line had three pairs of L. ponticum chromosomes from homoeologous chromosome groups 3, 5, and 6 and the 2n = 47 progeny had an additional L. ponticum monosome. The pairs from groups 3 and 6 were in the added state, while the group 5 pair was substituted for wheat chromosome 5D. Several wheat-wheat translocations with respect to the parental wheat genotype occurred in this line, presumably owing to the promotion of homoeologous chromosome pairing by L. ponticum chromosomes. It was hypothesized that homoeologous recombination results in homoeologous duplication-deletions in wheat chromosomes. An aberrant 3:1 disjunction creates the potential at each meiosis for replacement of these wheat chromosomes by homoeologous L. ponticum chromosomes. Wheat chromosomes 3A and 6A appeared to be in intermediate stages of this substitution process.
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Chao S, Lazo GR, You F, Crossman CC, Hummel DD, Lui N, Laudencia-Chingcuanco D, Anderson JA, Close TJ, Dubcovsky J, Gill BS, Gill KS, Gustafson JP, Kianian SF, Lapitan NLV, Nguyen HT, Sorrells ME, McGuire PE, Qualset CO, Anderson OD. Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.). Genome 2006; 49:531-44. [PMID: 16767178 DOI: 10.1139/g06-003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116,272 ESTs were produced, comprising 100,674 5' ESTs and 15 598 3' ESTs. These ESTs were derived from 42 cDNA libraries, which were created from hexaploid bread wheat (Triticum aestivum L.) and its close relatives, including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), using tissues collected from various stages of plant growth and development and under diverse regimes of abiotic and biotic stress treatments. ESTs were assembled into 18,876 contigs and 23,034 singletons, or 41,910 wheat unigenes. Over 90% of the contigs contained fewer than 10 EST members, implying that the ESTs represented a diverse selection of genes and that genes expressed at low and moderate to high levels were well sampled. Statistical methods were used to study the correlation of gene expression patterns, based on the ESTs clustered in the 1536 contigs that contained at least 10 5' EST members and thus representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly upregulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, it is likely that they play a role associated with the stress response. This study predicted the possible functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional roles and expression patterns largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.
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Affiliation(s)
- S Chao
- US Department of Agriculture - Agricultural Research Service (USAD-ARS), Western Regional Research Center, Albany, CA 94170, USA
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3
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Randhawa HS, Dilbirligi M, Sidhu D, Erayman M, Sandhu D, Bondareva S, Chao S, Lazo GR, Anderson OD, Gustafson JP, Echalier B, Qi LL, Gill BS, Akhunov ED, Dvorák J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Sorrells ME, Conley EJ, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Nguyen HT, Endo TR, Close TJ, McGuire PE, Qualset CO, Gill KS. Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags. Genetics 2005; 168:677-86. [PMID: 15514044 PMCID: PMC1448826 DOI: 10.1534/genetics.104.034843] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.
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Affiliation(s)
- H S Randhawa
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420, USA
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4
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Zhang D, Choi DW, Wanamaker S, Fenton RD, Chin A, Malatrasi M, Turuspekov Y, Walia H, Akhunov ED, Kianian P, Otto C, Simons K, Deal KR, Echenique V, Stamova B, Ross K, Butler GE, Strader L, Verhey SD, Johnson R, Altenbach S, Kothari K, Tanaka C, Shah MM, Laudencia-Chingcuanco D, Han P, Miller RE, Crossman CC, Chao S, Lazo GR, Klueva N, Gustafson JP, Kianian SF, Dubcovsky J, Walker-Simmons MK, Gill KS, Dvorák J, Anderson OD, Sorrells ME, McGuire PE, Qualset CO, Nguyen HT, Close TJ. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.). Genetics 2005; 168:595-608. [PMID: 15514038 PMCID: PMC1448820 DOI: 10.1534/genetics.104.034785] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.
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Affiliation(s)
- D Zhang
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409, USA
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5
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Linkiewicz AM, Qi LL, Gill BS, Ratnasiri A, Echalier B, Chao S, Lazo GR, Hummel DD, Anderson OD, Akhunov ED, Dvorák J, Pathan MS, Nguyen HT, Peng JH, Lapitan NLV, Gustafson JP, La Rota CM, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Bondareva SN, Gill KS, Conley EJ, Anderson JA, Fenton RD, Close TJ, McGuire PE, Qualset CO, Dubcovsky J. A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 2005; 168:665-76. [PMID: 15514043 PMCID: PMC1448825 DOI: 10.1534/genetics.104.034835] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible for these differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci, and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. Good overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).
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Affiliation(s)
- A M Linkiewicz
- Department of Agronomy and Range Science, University of California, Davis, California 95616, USA
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6
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Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorák J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 2005; 168:701-12. [PMID: 15514046 PMCID: PMC1448828 DOI: 10.1534/genetics.104.034868] [Citation(s) in RCA: 348] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.
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Affiliation(s)
- L L Qi
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502, USA
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7
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Hossain KG, Kalavacharla V, Lazo GR, Hegstad J, Wentz MJ, Kianian PMA, Simons K, Gehlhar S, Rust JL, Syamala RR, Obeori K, Bhamidimarri S, Karunadharma P, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Akhunov ED, Dvorák J, Miftahudin, Ross K, Gustafson JP, Radhawa HS, Dilbirligi M, Gill KS, Peng JH, Lapitan NLV, Greene RA, Bermudez-Kandianis CE, Sorrells ME, Feril O, Pathan MS, Nguyen HT, Gonzalez-Hernandez JL, Conley EJ, Anderson JA, Choi DW, Fenton D, Close TJ, McGuire PE, Qualset CO, Kianian SF. A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7. Genetics 2004; 168:687-99. [PMID: 15514045 PMCID: PMC1448827 DOI: 10.1534/genetics.104.034850] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Accepted: 06/01/2004] [Indexed: 01/16/2023] Open
Abstract
The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.
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Affiliation(s)
- K G Hossain
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105, USA
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8
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Peng JH, Zadeh H, Lazo GR, Gustafson JP, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Dilbirligi M, Sandhu D, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvorák J, Linkiewicz AM, Dubcovsky J, Hossain KG, Kalavacharla V, Kianian SF, Mahmoud AA, Miftahudin, Conley EJ, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Lapitan NLV. Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 2004; 168:609-23. [PMID: 15514039 PMCID: PMC1448821 DOI: 10.1534/genetics.104.034793] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Accepted: 06/01/2004] [Indexed: 11/18/2022] Open
Abstract
A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E < or = 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.
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Affiliation(s)
- J H Peng
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170, USA
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9
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Munkvold JD, Greene RA, Bermudez-Kandianis CE, La Rota CM, Edwards H, Sorrells SF, Dake T, Benscher D, Kantety R, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorák J, Miftahudin, Gustafson JP, Pathan MS, Nguyen HT, Matthews DE, Chao S, Lazo GR, Hummel DD, Anderson OD, Anderson JA, Gonzalez-Hernandez JL, Peng JH, Lapitan N, Qi LL, Echalier B, Gill BS, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Erayman M, Gill KS, McGuire PE, Qualset CO, Sorrells ME. Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 2004; 168:639-50. [PMID: 15514041 PMCID: PMC1448823 DOI: 10.1534/genetics.104.034819] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Accepted: 06/01/2004] [Indexed: 01/24/2023] Open
Abstract
The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes approximately 21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.
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Affiliation(s)
- J D Munkvold
- Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
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10
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Lazo GR, Chao S, Hummel DD, Edwards H, Crossman CC, Lui N, Matthews DE, Carollo VL, Hane DL, You FM, Butler GE, Miller RE, Close TJ, Peng JH, Lapitan NLV, Gustafson JP, Qi LL, Echalier B, Gill BS, Dilbirligi M, Randhawa HS, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvorák J, Linkiewicz AM, Dubcovsky J, Hossain KG, Kalavacharla V, Kianian SF, Mahmoud AA, Miftahudin, Ma XF, Conley EJ, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Anderson OD. 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 2004; 168:585-93. [PMID: 15514037 PMCID: PMC1448819 DOI: 10.1534/genetics.104.034777] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Accepted: 06/01/2004] [Indexed: 01/06/2023] Open
Abstract
This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.
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Affiliation(s)
- G R Lazo
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Western Regional Research Center, Albany, California 94710-1105, USA
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11
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Miftahudin, Ross K, Ma XF, Mahmoud AA, Layton J, Milla MAR, Chikmawati T, Ramalingam J, Feril O, Pathan MS, Momirovic GS, Kim S, Chema K, Fang P, Haule L, Struxness H, Birkes J, Yaghoubian C, Skinner R, McAllister J, Nguyen V, Qi LL, Echalier B, Gill BS, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorák J, Dilbirligi M, Gill KS, Peng JH, Lapitan NLV, Bermudez-Kandianis CE, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Lazo GR, Chao S, Anderson OD, Gonzalez-Hernandez J, Conley EJ, Anderson JA, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Nguyen HT, Gustafson JP. Analysis of expressed sequence tag loci on wheat chromosome group 4. Genetics 2004; 168:651-63. [PMID: 15514042 PMCID: PMC1448824 DOI: 10.1534/genetics.104.034827] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 06/01/2004] [Indexed: 12/16/2022] Open
Abstract
A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.
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Affiliation(s)
- Miftahudin
- Department of Agronomy, University of Missouri, Columbia, Missouri 65211, USA
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Conley EJ, Nduati V, Gonzalez-Hernandez JL, Mesfin A, Trudeau-Spanjers M, Chao S, Lazo GR, Hummel DD, Anderson OD, Qi LL, Gill BS, Echalier B, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorák J, Peng JH, Lapitan NLV, Pathan MS, Nguyen HT, Ma XF, Miftahudin, Gustafson JP, Greene RA, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sidhu D, Dilbirligi M, Gill KS, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Anderson JA. A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics 2004; 168:625-37. [PMID: 15514040 PMCID: PMC1448822 DOI: 10.1534/genetics.104.034801] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 06/01/2004] [Indexed: 11/18/2022] Open
Abstract
The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.
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Affiliation(s)
- E J Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
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Sorrells ME, Anderson OD, Baenziger PS, Cook RJ, Cregan PB, Dubcovsky J, Dvorak J, Gill BS, Hart GE, Hayes PM, Herman EM, Kleinhofs A, Line RF, Qualset CO, McGuire PE. Corn genome initiative. Science 1997; 277:884-5. [PMID: 9281064 DOI: 10.1126/science.277.5328.883d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Kota RS, McGuire PE, Dvorák J. Latent Nonstructural Differentiation among Homologous Chromosomes at the Diploid Level: Chromosome 6B of AEGILOPS LONGISSIMA. Genetics 1986; 114:579-92. [PMID: 17246349 PMCID: PMC1202958 DOI: 10.1093/genetics/114.2.579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous work has shown that chromosome pairing at metaphase I (MI) of wheat homologous chromosomes from different inbred lines (heterohomologous chromosomes) is reduced relative to that between homologous chromosomes within an inbred line (euhomologous chromosomes). In order to determine if a potential for this phenomenon exists in diploid species closely related to the wheat B genome, MI chromosome pairing was investigated between euhomologous and heterohomologous 6B(e) (=6S(e)) chromosomes, each from a different population of Aegilops longissima Schweinf. et Muschl. (2n = 2x = 14) substituted for chromosome 6B of Chinese Spring wheat (Triticum aestivum L., 2n = 6x = 42). Euhomologous and heterohomologous monotelodisomics, i.e., plants with one complete chromosome 6B(e) and a telosome of either 6B(e)p or 6B(e)q, were constructed in the isogenic background of Chinese Spring. Pairing at MI of the Ae. longissima chromosomes was reduced in heterohomologous monotelodisomics compared to that in the corresponding euhomologous monotelodisomics. The remaining 20 pairs of Chinese Spring chromosomes paired equally well in the euhomologous and heterohomologous monotelodisomics. Thus, the cause of the reduced pairing must reside specifically in the Ae. longissima heterohomologues. In the hybrids between the Ae. longissima lines that contributed the substituted chromosomes, pairing between the heterohomologous chromosomes was normal and did not differ from that of the euhomologous chromosomes. These data provide evidence that a potential for reduced pairing between the heterohomologues is present in the diploid species, but is expressed only in the polyploid wheat genetic background. The reduction in heterohomologous chromosome pairing was greater in the p arm than in the q arm, exactly as in chromosome 6B of wheat. It is concluded that the reduced pairing between Ae. longissima heterohomologues has little to do with constitutive heterochromatin. The value of chromosome pairing as an unequivocal means of determining the origin of genomes in polyploid plants is questioned.
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Affiliation(s)
- R S Kota
- Department of Agronomy and Range Science, University of California, Davis, California 95616
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McGuire PE, Dvorák J. RELATIONSHIP BETWEEN THE NUMBER OF HOMOEOLOGUES, CHIASMA FREQUENCY AND THE FREQUENCY OF TELOSOME PAIRING IN WHEAT. Genetics 1981; 98:589-96. [PMID: 17249101 PMCID: PMC1214460 DOI: 10.1093/genetics/98.3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Pairing frequencies of a single telosome in groups of two, three, four, five and six equally related homoeologues were calculated for a range of values of c (the ratio of actual chiasma frequency to the total possible number of chiasmata, as described by Driscoll, Bielig and Darvey 1979). At low c values, the frequency of telosome pairing is little affected by the number of homoeologues. At high c values, the frequency is little affected by the number of homoeolgues if the number is even; if the number is odd, the frequency is dependent on the number of homoeologues and increases with increasing numbers of homoeologues. At intermediate c values, the pairing frequency is dependent on the number of homoeologues for both even and odd numbers of homoeologues.
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Affiliation(s)
- P E McGuire
- Department of Agronomy, University of California, Davis, California 95616
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Dvorák J, McGuire PE. NONSTRUCTURAL CHROMOSOME DIFFERENTIATION AMONG WHEAT CULTIVARS, WITH SPECIAL REFERENCE TO DIFFERENTIATION OF CHROMOSOMES IN RELATED SPECIES. Genetics 1981; 97:391-414. [PMID: 17249077 PMCID: PMC1214400 DOI: 10.1093/genetics/97.2.391] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Wheat cultivar Chinese Spring (Triticum aestivum L. em. Thell.) was crossed with cultivars Hope, Cheyenne and Timstein. In all three hybrids, the frequencies of pollen mother cells (PMCs) with univalents at metaphase I (MI) were higher than those in the parental cultivars. No multivalents were observed in the hybrids, indicating that the cultivars do not differ by translocations. Thirty-one Chinese Spring telosomic lines were then crossed with substitution lines in which single chromosomes of the three cultivars were substituted for their Chinese Spring homologues. The telosomic lines were also crossed with Chinese Spring. Data were collected on the frequencies (% of PMCs) of pairing of the telesomes with their homologues at MI and the regularity of pairing of the remaining 20 pairs of Chinese Spring chromosomes in the monotelodisomics obtained from these crosses. The reduced MI pairing in the intercultivar hybrids was caused primarily by chromosome differentiation, rather than by specific genes. Because the differentiation involved a large part of the chromosome complement in each hybrid, it was concluded that it could not be caused by structural changes such as inversions or translocations. In each case, the differentiation appeared to be unevenly distributed among the three wheat genomes. It is proposed that the same kind of differentiation, although of greater magnitude, differentiates homoeologous chromosomes and is responsible, together with structural differentiation, for poor chromosome pairing in interspecific hybrids.
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Affiliation(s)
- J Dvorák
- Department of Agronomy, University of California, Davis, California 95616
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