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Yang S, Zeng K, Luo L, Qian W, Wang Z, Doležel J, Zhang M, Gao X, Deng Z. A flow cytometry-based analysis to establish a cell cycle synchronization protocol for Saccharum spp. Sci Rep 2020; 10:5016. [PMID: 32193460 PMCID: PMC7081271 DOI: 10.1038/s41598-020-62086-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/09/2020] [Indexed: 11/09/2022] Open
Abstract
Modern sugarcane is an unusually complex heteroploid crop, and its genome comprises two or three subgenomes. To reduce the complexity of sugarcane genome research, the ploidy level and number of chromosomes can be reduced using flow chromosome sorting. However, a cell cycle synchronization (CCS) protocol for Saccharum spp. is needed that maximizes the accumulation of metaphase chromosomes. For flow cytometry analysis in this study, we optimized the lysis buffer, hydroxyurea(HU) concentration, HU treatment time and recovery time for sugarcane. We determined the mitotic index by microscopic observation and calculation. We found that WPB buffer was superior to other buffers for preparation of sugarcane nuclei suspensions. The optimal HU treatment was 2 mM for 18 h at 25 °C, 28 °C and 30 °C. Higher recovery treatment temperatures were associated with shorter recovery times (3.5 h, 2.5 h and 1.5 h at 25 °C, 28 °C and 30 °C, respectively). The optimal conditions for treatment with the inhibitor of microtubule polymerization, amiprophos-methyl (APM), were 2.5 μM for 3 h at 25 °C, 28 °C and 30 °C. Meanwhile, preliminary screening of CCS protocols for Badila were used for some main species of genus Saccharum at 25 °C, 28 °C and 30 °C, which showed that the average mitotic index decreased from 25 °C to 30 °C. The optimal sugarcane CCS protocol that yielded a mitotic index of >50% in sugarcane root tips was: 2 mM HU for 18 h, 0.1 X Hoagland's Solution without HU for 3.5 h, and 2.5 μM APM for 3.0 h at 25 °C. The CCS protocol defined in this study should accelerate the development of genomic research and cytobiology research in sugarcane.
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Affiliation(s)
- Shan Yang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Zeng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ling Luo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wang Qian
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiqiang Wang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Olomouc, CZ-78371, Czech Republic
| | - Muqing Zhang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
| | - Xiangxiong Gao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory for Protection and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
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Ivanizs L, Farkas A, Linc G, Molnár-Láng M, Molnár I. Molecular cytogenetic and morphological characterization of two wheat-barley translocation lines. PLoS One 2018; 13:e0198758. [PMID: 29889875 PMCID: PMC5995406 DOI: 10.1371/journal.pone.0198758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/24/2018] [Indexed: 11/18/2022] Open
Abstract
Barley chromosome 5H, carrying important QTLs for plant adaptation and tolerance to abiotic stresses, is extremely instable in the wheat genetic background and is eliminated in the early generations of wheat-barley crosses. A spontaneous wheat-barley 5HS-7DS.7DL translocation was previously obtained among the progenies of the Mv9kr1 x Igri hybrid. The present work reports on the transfer of the 5HS-7DS.7DL translocation into a modern wheat cultivar, Mv Bodri, in order to use it in the wheat breeding program. The comparison of the hybridization bands of DNA repeats HvT01, pTa71, (GAA)n and the barley centromere-specific (AGGGAG)n in Igri barley and the 5HS-7DS.7DL translocation, together with the visualization of the barley chromatin made it possible to determine the size of the introgressed barley segment, which was approximately 74% of the whole 5HS. Of the 29 newly developed PCR markers, whose source ESTs were selected from the Genome Zipper of barley chromosome 5H, 23 were mapped in the introgressed 1-0.26 FL 5HS bin, three were located in the missing C-0.26 FL region, while three markers were specific for 5HL. The translocation breakpoint was flanked by markers Hv7502 and Hv3949. A comparison of the parental wheat cultivars and the wheat-barley introgression lines indicated that the presence of the translocation improved tillering ability in the Mv9kr1 and Mv Bodri genetic background. The similar or better yield components under high- or low-input cultivation environments, respectively, indicated that the 5HS-7DS.7DL translocation had little or no negative effect on yield components, making it a promising genotype to improve wheat genetic diversity. These results promise to accelerate functional genomic studies on barley chromosome 5H and to support pre-breeding and breeding research on wheat.
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Affiliation(s)
- László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - Gabriella Linc
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Brunszvik u. 2, Hungary
- Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc-Holice, Czech Republic
- * E-mail:
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Li Q, Lu Y, Pan C, Yao M, Zhang J, Yang X, Liu W, Li X, Xi Y, Li L. Chromosomal Localization of Genes Conferring Desirable Agronomic Traits from Wheat-Agropyron cristatum Disomic Addition Line 5113. PLoS One 2016; 11:e0165957. [PMID: 27824906 PMCID: PMC5100930 DOI: 10.1371/journal.pone.0165957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/20/2016] [Indexed: 11/29/2022] Open
Abstract
Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F1, BC1F1 and BC1F2 populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding.
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Affiliation(s)
- Qingfeng Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cuili Pan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miaomiao Yao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Vrána J, Cápal P, Šimková H, Karafiátová M, Čížková J, Doležel J. Flow Analysis and Sorting of Plant Chromosomes. CURRENT PROTOCOLS IN CYTOMETRY 2016; 78:5.3.1-5.3.43. [PMID: 27723090 DOI: 10.1002/cpcy.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Türkösi E, Cseh A, Darkó É, Molnár-Láng M. Addition of Manas barley chromosome arms to the hexaploid wheat genome. BMC Genet 2016; 17:87. [PMID: 27328706 PMCID: PMC4915093 DOI: 10.1186/s12863-016-0393-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/07/2016] [Indexed: 01/04/2023] Open
Abstract
Background Cultivated barley belongs to the tertiary genepool of hexaploid wheat. Genes of interest can be transferred from barley into wheat through wide hybridization. The application of wheat-barley introgression lines could provide an excellent tool for the transfer of earliness, favourable amino acid composition, biotic stress resistance, abiotic stress tolerance, or good tillering ability into wheat. Results A set of 10 wheat-barley ditelosomic addition lines (2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 6HS, 6HL, 7HS and 7HL) was developed from the progenies of an Asakaze/Manas wheat-barley hybrid produced in Martonvásár, Hungary. The addition lines were selected from self-fertilized plants of the BC2F2-BC2F4 generations using genomic in situ hybridization (GISH) and were identified by fluorescence in situ hybridization (FISH) with repetitive DNA probes [HvT01, (GAA)7 and centromere-specific (AGGGAG)4 probes]. The cytogenetic identification was confirmed using barley arm-specific SSR and STS markers. The ditelosomic additions were propagated in the phytotron and in the field, and morphological parameters (plant height, tillering, length of the main spike, number of seeds/spike and seeds/plant, and spike characteristics) were described. In addition, the salt stress response of the ditelosomic additions was determined. Conclusions The six-rowed winter barley cultivar Manas is much better adapted to Central European environmental conditions than the two-rowed spring barley Betzes previously used in wheat-barley crosses. The production of wheat-barley ditelosomic addition lines has a wide range of applications both for breeding (transfer of useful genes to the recipient species) and for basic research (mapping of barley genes, genetic and evolutionary studies and heterologous expression of barley genes in the wheat background). Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0393-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edina Türkösi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, P.O. Box 19, Hungary
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, P.O. Box 19, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, P.O. Box 19, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, P.O. Box 19, Hungary.
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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Calderón MDC, Rey MD, Cabrera A, Prieto P. The subtelomeric region is important for chromosome recognition and pairing during meiosis. Sci Rep 2014; 4:6488. [PMID: 25270583 PMCID: PMC4180820 DOI: 10.1038/srep06488] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/10/2014] [Indexed: 12/26/2022] Open
Abstract
The process of meiosis results in the formation of haploid daughter cells, each of which inherit a half of the diploid parental cells' genetic material. The ordered association of homologues (identical chromosomes) is a critical prerequisite for a successful outcome of meiosis. Homologue recognition and pairing are initiated at the chromosome ends, which comprise the telomere dominated by generic repetitive sequences, and the adjacent subtelomeric region, which harbours chromosome-specific sequences. In many organisms telomeres are responsible for bringing the ends of the chromosomes close together during early meiosis, but little is known regarding the role of the subtelomeric region sequence during meiosis. Here, the observation of homologue pairing between a pair of Hordeum chilense chromosomes lacking the subtelomeric region on one chromosome arm indicates that the subtelomeric region is important for the process of homologous chromosome recognition and pairing.
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Affiliation(s)
- María del Carmen Calderón
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Apartado 4084, E-14080 Córdoba, Spain
| | - María-Dolores Rey
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Apartado 4084, E-14080 Córdoba, Spain
| | - Adoración Cabrera
- Department of Genetics, ETSIAM, University of Córdoba, Campus de Excelencia Internacional Agroalimentario, CeiA3, 14071 Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Apartado 4084, E-14080 Córdoba, Spain
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8
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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9
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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10
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Joshi GP, Endo TR, Nasuda S. PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2381-2390. [PMID: 23765160 DOI: 10.1007/s00122-013-2142-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/03/2013] [Indexed: 05/28/2023]
Abstract
Gametocidal (Gc) chromosomes induce various types of chromosomal mutations during gametogenesis in the chromosomes of common wheat and alien chromosomes added to common wheat. However, it is not yet known whether the Gc chromosome causes aberrations at the nucleotide level because mutations caused by Gc chromosomes have been studied only by cytological screening. In order to know whether the Gc chromosome induces point mutations, we conducted PCR analysis and sequencing with the progeny of a common wheat line that is disomic for barley chromosome 2H and monosomic for Gc chromosome 2C. We analyzed 18 2H-specific EST sequences using 81 progeny plants carrying a cytologically normal-appearing 2H chromosome and found no nucleotide changes in the analyzed 1,419 sequences (in total 647,075 bp). During this analysis, we found six plants for which some ESTs could not be PCR amplified, suggesting the presence of chromosomal mutations in these plants. The cytological and PCR analyses of the progeny of the six plants confirmed the occurrence of chromosomal mutations in the parental plants. These results suggested that the Gc chromosome mostly induced chromosomal aberrations, not nucleotide changes, and that the Gc-induced chromosomal mutations in the six plants occurred after fertilization.
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Affiliation(s)
- Giri Prasad Joshi
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto, Japan
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11
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Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis MM, Graner A, Schweizer P, Scholz U, Mayer K, Stein N. Conserved synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 2013. [PMID: 23812960 DOI: 10.1007/s10142‐013‐0327‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene locations obtained from the maps constructed in other grass species, was evaluated here both at the genome-wide level and at the fine scale in a representative segment of the genome. Comparing the whole genome "genome zipper" maps with a genetic map developed by using transcript-derived markers, yielded an accuracy of >94 %. The fine-scale comparison involved a 14 cM segment of chromosome arm 2HL. One hundred twenty-eight genes of the "genome zipper" interval were analysed. Over 95 % (45/47) of the polymorphic markers were genetically mapped and allocated to the expected region of 2HL, following the predicted order. A further 80 of the 128 genes were assigned to the correct chromosome arm 2HL by analysis of wheat-barley addition lines. All 128 gene-based markers developed were used to probe a barley bacterial artificial chromosome (BAC) library, delivering 26 BAC contigs from which all except two were anchored to the targeted zipper interval. The results demonstrate that the gene order predicted by the "genome zipper" is remarkably accurate and that the "genome zipper" represents a highly efficient informational resource for the systematic identification of gene-based markers and subsequent physical map anchoring of the barley genome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research-IPK, Corrensstr. 3, 06466 Seeland, OT, Gatersleben, Germany
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12
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Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis MM, Graner A, Schweizer P, Scholz U, Mayer K, Stein N. Conserved synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 2013; 13:339-50. [PMID: 23812960 DOI: 10.1007/s10142-013-0327-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/17/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene locations obtained from the maps constructed in other grass species, was evaluated here both at the genome-wide level and at the fine scale in a representative segment of the genome. Comparing the whole genome "genome zipper" maps with a genetic map developed by using transcript-derived markers, yielded an accuracy of >94 %. The fine-scale comparison involved a 14 cM segment of chromosome arm 2HL. One hundred twenty-eight genes of the "genome zipper" interval were analysed. Over 95 % (45/47) of the polymorphic markers were genetically mapped and allocated to the expected region of 2HL, following the predicted order. A further 80 of the 128 genes were assigned to the correct chromosome arm 2HL by analysis of wheat-barley addition lines. All 128 gene-based markers developed were used to probe a barley bacterial artificial chromosome (BAC) library, delivering 26 BAC contigs from which all except two were anchored to the targeted zipper interval. The results demonstrate that the gene order predicted by the "genome zipper" is remarkably accurate and that the "genome zipper" represents a highly efficient informational resource for the systematic identification of gene-based markers and subsequent physical map anchoring of the barley genome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research-IPK, Corrensstr. 3, 06466 Seeland, OT, Gatersleben, Germany
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13
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Doležel J, Vrána J, Safář J, Bartoš J, Kubaláková M, Simková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012; 12:397-416. [PMID: 22895700 PMCID: PMC3431466 DOI: 10.1007/s10142-012-0293-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
Abstract
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
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Affiliation(s)
- Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, Czech Republic.
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Molnár-Láng M, Kruppa K, Cseh A, Bucsi J, Linc G. Identification and phenotypic description of new wheat – six-rowed winter barley disomic additions. Genome 2012; 55:302-11. [DOI: 10.1139/g2012-013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
To increase the allelic variation in wheat–barley introgressions, new wheat–barley disomic addition lines were developed containing the 2H, 3H, 4H, 6H, and 7H chromosomes of the six-rowed Ukrainian winter barley ‘Manas’. This cultivar is agronomically much better adapted to Central European environmental conditions than the two-rowed spring barley ‘Betzes’ previously used. A single ‘Asakaze’ × ‘Manas’ wheat × barley hybrid plant was multiplied in vitro and one backcross plant was obtained after pollinating 354 regenerant hybrids with wheat. The addition lines were selected from the self-fertilized seeds of the 16 BC2 plants using genomic in situ hybridization. The addition lines were identified by fluorescence in situ hybridization using repetitive DNA probes (HvT01, GAA, pTa71, and Afa family), followed by confirmation with barley SSR markers. The addition lines were grown in the phytotron and in the field, and morphological parameters (plant height, fertility, tillering, and spike characteristics) were measured. The production of the disomic additions will make it possible to incorporate the DNA of six-rowed winter barley into the wheat genome. Addition lines are useful for genetic studies on the traits of six-rowed winter barley and for producing new barley dissection lines.
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Affiliation(s)
- Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, POB 19, Hungary
| | - Klaudia Kruppa
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, POB 19, Hungary
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, POB 19, Hungary
| | - Julianna Bucsi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, POB 19, Hungary
| | - Gabriella Linc
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, POB 19, Hungary
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15
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Vrána J, Simková H, Kubaláková M, Cíhalíková J, Doležel J. Flow cytometric chromosome sorting in plants: the next generation. Methods 2012; 57:331-7. [PMID: 22440520 DOI: 10.1016/j.ymeth.2012.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 03/01/2012] [Accepted: 03/05/2012] [Indexed: 10/28/2022] Open
Abstract
Genome analysis in many plant species is hampered by large genome size and by sequence redundancy due to the presence of repetitive DNA and polyploidy. One solution is to reduce the sample complexity by dissecting the genomes to single chromosomes. This can be realized by flow cytometric sorting, which enables purification of chromosomes in large numbers. Coupling the chromosome sorting technology with next generation sequencing provides a targeted and cost effective way to tackle complex genomes. The methods outlined in this article describe a procedure for preparation of chromosomal DNA suitable for next-generation sequencing.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic
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16
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Cseh A, Kruppa K, Molnár I, Rakszegi M, Doležel J, Molnár-Láng M. Characterization of a new 4BS.7HL wheat–barley translocation line using GISH, FISH, and SSR markers and its effect on the β-glucan content of wheat. Genome 2011; 54:795-804. [DOI: 10.1139/g11-044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A spontaneous interspecific Robertsonian translocation was revealed by genomic in situ hybridization (GISH) in the progenies of a monosomic 7H addition line originating from a new wheat ‘Asakaze komugi’ × barley ‘Manas’ hybrid. Fluorescence in situ hybridization (FISH) with repetitive DNA sequences (Afa family, pSc119.2, and pTa71) allowed identification of all wheat chromosomes, including wheat chromosome arm 4BS involved in the translocation. FISH using barley telomere- and centromere-specific repetitive DNA probes (HvT01 and (AGGGAG)n) confirmed that one of the arms of barley chromosome 7H was involved in the translocation. Simple sequence repeat (SSR) markers specific to the long (L) and short (S) arms of barley chromosome 7H identified the translocated chromosome segment as 7HL. Further analysis of the translocation chromosome clarified the physical position of genetically mapped SSRs within 7H, with a special focus on its centromeric region. The presence of the HvCslF6 gene, responsible for (1,3;1,4)-β-d-glucan production, was revealed in the centromeric region of 7HL. An increased (1,3;1,4)-β-d-glucan level was also detected in the translocation line, demonstrating that the HvCslF6 gene is of potential relevance for the manipulation of wheat (1,3;1,4)-β-d-glucan levels.
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Affiliation(s)
- A. Cseh
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - K. Kruppa
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - I. Molnár
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - M. Rakszegi
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
| | - J. Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - M. Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvásár, PO Box 19, Hungary
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17
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Zatloukalová P, Hřibová E, Kubaláková M, Suchánková P, Simková H, Adoración C, Kahl G, Millán T, Doležel J. Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. Chromosome Res 2011; 19:729-39. [PMID: 21947955 DOI: 10.1007/s10577-011-9235-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 08/20/2011] [Accepted: 08/23/2011] [Indexed: 11/29/2022]
Abstract
Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.
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Affiliation(s)
- Pavlína Zatloukalová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Sokolovská 6, 77200 Olomouc, Czech Republic
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18
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Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. THE PLANT CELL 2011; 23:1706-18. [PMID: 21622801 PMCID: PMC3123954 DOI: 10.1105/tpc.111.086629] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/19/2011] [Accepted: 05/16/2011] [Indexed: 05/18/2023]
Abstract
All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Klaus F.X. Mayer
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Mihaela Martis
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Frédéric Choulet
- Institut National de la Recherche Agronomique University Blaise Pascal Joint Research Unit 1095, Genetics, Diversity, and Ecophysiology of Cereals, 63100 Clermont-Ferrand, France
| | - Stefan Taudien
- Leibniz Institute for Age Research–Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research–Fritz Lipmann Institute, 07745 Jena, Germany
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique University Blaise Pascal Joint Research Unit 1095, Genetics, Diversity, and Ecophysiology of Cereals, 63100 Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Hikmet Budak
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
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Mayer KF, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N. Unlocking the barley genome by chromosomal and comparative genomics. THE PLANT CELL 2011; 23:1249-63. [PMID: 21467582 PMCID: PMC3101540 DOI: 10.1105/tpc.110.082537] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/10/2011] [Accepted: 03/18/2011] [Indexed: 05/18/2023]
Abstract
We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
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Affiliation(s)
- Klaus F.X. Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Mihaela Martis
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Pete E. Hedley
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Hui Liu
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Jenny A. Morris
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Stefan Taudien
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Stephan Roessner
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Pavla Suchánková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Florent Murat
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Marius Felder
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Thomas Nussbaumer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jerome Salse
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Takashi Endo
- Kyoto University, Laboratory of Plant Genetics, Kyoto 606-8502, Japan
| | - Hiroaki Sakai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Tsuyoshi Tanaka
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazuhiro Sato
- Okayama University, Institute of Plant Science and Resources, Kurashiki 710-0046, Japan
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Robbie Waugh
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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Doležel J, Kubaláková M, Cíhalíková J, Suchánková P, Simková H. Chromosome analysis and sorting using flow cytometry. Methods Mol Biol 2011; 701:221-38. [PMID: 21181533 DOI: 10.1007/978-1-61737-957-4_12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Chromosome analysis and sorting using flow cytometry (flow cytogenetics) is an attractive tool for fractionating plant genomes to small parts. The reduction of complexity greatly simplifies genetics and genomics in plant species with large genomes. However, as flow cytometry requires liquid suspensions of particles, the lack of suitable protocols for preparation of solutions of intact chromosomes delayed the application of flow cytogenetics in plants. This chapter outlines a high-yielding procedure for preparation of solutions of intact mitotic chromosomes from root tips of young seedlings and for their analysis using flow cytometry and sorting. Root tips accumulated at metaphase are mildly fixed with formaldehyde, and solutions of intact chromosomes are prepared by mechanical homogenization. The advantages of the present approach include the use of seedlings, which are easy to handle, and the karyological stability of root meristems, which can be induced to high degree of metaphase synchrony. Chromosomes isolated according to this protocol have well-preserved morphology, withstand shearing forces during sorting, and their DNA is intact and suitable for a range of applications.
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Affiliation(s)
- Jaroslav Doležel
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic.
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21
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Rustenholz C, Hedley PE, Morris J, Choulet F, Feuillet C, Waugh R, Paux E. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources. BMC Genomics 2010; 11:714. [PMID: 21167071 PMCID: PMC3019236 DOI: 10.1186/1471-2164-11-714] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/19/2010] [Indexed: 11/16/2022] Open
Abstract
Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
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Affiliation(s)
- Camille Rustenholz
- INRA UMR 1095, Génétique Diversité et Ecophysiologie des Céréales, 63100 Clermont-Ferrand, France
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Szakács É, Molnár-Láng M. Identification of new winter wheat – winter barley addition lines (6HS and 7H) using fluorescence in situ hybridization and the stability of the whole ‘Martonvásári 9 kr1’ – ‘Igri’ addition set. Genome 2010; 53:35-44. [DOI: 10.1139/g09-085] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A previous paper reported the development of disomic addition lines (2H, 3H, 4H, and 1HS isochromosomic) from hybrids between the winter wheat ‘Martonvásári 9 kr1’ and the two-rowed winter barley cultivar ‘Igri’. The present paper describes the isolation of two new additions, the 7H disomic and 6HS ditelosomic additions, using fluorescence in situ hybridization with the repetitive DNA probes Afa-family and HvT01. The identification of the barley chromosomes in the wheat genome was confirmed with simple sequence repeat markers. The morphological characterization of the new addition lines is also discussed. Studies of the genetic stability of the whole set (2H, 3H, 4H, 7H, 1HS iso, 6HS) of ‘Martonvásári 9 kr1’ – ‘Igri’ additions revealed that the most stable disomic additions are 2H and 3H and the most unstable line is the 1HS isochromosomic addition.
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Affiliation(s)
- É. Szakács
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462 Martonvásár, P.O. Box 19, Hungary
| | - M. Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462 Martonvásár, P.O. Box 19, Hungary
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Mayer KFX, Taudien S, Martis M, Simková H, Suchánková P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N. Gene content and virtual gene order of barley chromosome 1H. PLANT PHYSIOLOGY 2009; 151:496-505. [PMID: 19692534 PMCID: PMC2754631 DOI: 10.1104/pp.109.142612] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2009] [Accepted: 08/13/2009] [Indexed: 05/18/2023]
Abstract
Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.
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Affiliation(s)
- Klaus F X Mayer
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Abstract
Since the first report on the flow cytometric study of plant material 35 years ago, analyzing the nuclear DNA content of field bean, an ever increasing number of applications of FCM has been developed and applied in plant science and industry, but a similar length of time elapsed before the appearance of the first complete volume devoted to FCM of plant cells. Most published information on the uses of FCM addresses various aspects of animal (including human) cell biology, thus failing to provide a pertinent substitute. FCM represents an ideal means for the analysis of both cells and subcellular particles, with a potentially large number of parameters analyzed both rapidly, simultaneously, and quantitatively, thereby furnishing statistically exploitable data and allowing for an accurate and facilitated detection of subpopulations. It is, indeed, the summation of these facts that has established FCM as an important, and sometimes essential, tool for the understanding of fundamental mechanisms and processes underlying plant growth, development, and function. In this review, special attention is paid to FCM as applied to plant cells in the context of plant breeding, and some new and less well-known uses of it for plants will be discussed.
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Affiliation(s)
- Sergio J Ochatt
- INRA, C.R. Dijon, Unité Mixte de Recherches en Génétique et Ecophysiologie des Légumineuses, Dijon Cedex, France.
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25
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Simková H, Svensson JT, Condamine P, Hribová E, Suchánková P, Bhat PR, Bartos J, Safár J, Close TJ, Dolezel J. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genomics 2008; 9:294. [PMID: 18565235 PMCID: PMC2453526 DOI: 10.1186/1471-2164-9-294] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 06/19/2008] [Indexed: 01/06/2023] Open
Abstract
Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA). Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA) for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which considerably expands the potential of chromosome flow sorting in plant genomics.
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Affiliation(s)
- Hana Simková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic.
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26
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Simková H, Svensson JT, Condamine P, Hribová E, Suchánková P, Bhat PR, Bartos J, Safár J, Close TJ, Dolezel J. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genomics 2008. [PMID: 18565235 DOI: 10.1186/1471‐2164‐9‐294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. RESULTS Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA). Overnight amplification in a 20-microlitre reaction produced 3.7 - 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA) for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H - 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. CONCLUSION The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which considerably expands the potential of chromosome flow sorting in plant genomics.
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Affiliation(s)
- Hana Simková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic.
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Simková H, Safár J, Suchánková P, Kovárová P, Bartos J, Kubaláková M, Janda J, Cíhalíková J, Mago R, Lelley T, Dolezel J. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS). BMC Genomics 2008; 9:237. [PMID: 18495015 PMCID: PMC2410134 DOI: 10.1186/1471-2164-9-237] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 05/21/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. RESULTS We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. CONCLUSION We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.
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Affiliation(s)
- Hana Simková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic.
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Ribeiro T, Barão A, Viegas W, Morais-Cecíli L. Molecular cytogenetics of forest trees. Cytogenet Genome Res 2008; 120:220-7. [DOI: 10.1159/000121070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2007] [Indexed: 01/03/2023] Open
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Affiliation(s)
- Pablo D Rabinowicz
- J. C. Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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30
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Abstract
The cereals are of enormous importance to mankind. Many of the major cereal species - specifically, wheat, barley, oat, rye, and maize - have large genomes. Early cytogenetics, genome analysis and genetic mapping in the cereals benefited greatly from their large chromosomes, and the allopolyploidy of wheat and oats that has allowed for the development of many precise cytogenetic stocks. In the genomics era, however, large genomes are disadvantageous. Sequencing large and complex genomes is expensive, and the assembly of genome sequence is hampered by a significant content of repetitive DNA and, in allopolyploids, by the presence of homoeologous genomes. Dissection of the genome into its component chromosomes and chromosome arms provides an elegant solution to these problems. In this review we illustrate how this can be achieved by flow cytometric sorting. We describe the development of methods for the preparation of intact chromosome suspensions from the major cereals, and their analysis and sorting using flow cytometry. We explain how difficulties in the discrimination of specific chromosomes and their arms can be overcome by exploiting extant cytogenetic stocks of polyploid wheat and oats, in particular chromosome deletion and alien addition lines. Finally, we discuss some of the applications of flow-sorted chromosomes, and present some examples demonstrating that a chromosome-based approach is advantageous for the analysis of the complex genomes of cereals, and that it can offer significant potential for the delivery of genome sequencing and gene cloning in these crops.
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Affiliation(s)
- Jaroslav Dolezel
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic.
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