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Neděla V, Tihlaříková E, Cápal P, Doležel J. Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state. Sci Rep 2024; 14:12998. [PMID: 38844535 PMCID: PMC11156959 DOI: 10.1038/s41598-024-63515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
The challenge of in-situ handling and high-resolution low-dose imaging of intact, sensitive and wet samples in their native state at nanometer scale, including live samples is met by Advanced Environmental Scanning Electron Microscopy (A-ESEM). This new generation of ESEM utilises machine learning-based optimization of thermodynamic conditions with respect to sample specifics to employ a low temperature method and an ionization secondary electron detector with an electrostatic separator. A modified electron microscope was used, equipped with temperature, humidity and gas pressure sensors for in-situ and real-time monitoring of the sample. A transparent ultra-thin film of ionic liquid is used to increase thermal and electrical conductivity of the samples and to minimize sample damage by free radicals. To validate the power of the new method, we analyze condensed mitotic metaphase chromosomes to reveal new structural features of their perichromosomal layer, and the organization of chromatin fibers, not observed before by any microscopic technique. The ability to resolve nano-structural details of chromosomes using A-ESEM is validated by measuring gold nanoparticles with achievable resolution in the lower nanometre units.
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Affiliation(s)
- Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic.
| | - Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
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Tounsi S, Giorgi D, Kuzmanović L, Jrad O, Farina A, Capoccioni A, Ben Ayed R, Brini F, Ceoloni C. Coping with salinity stress: segmental group 7 chromosome introgressions from halophytic Thinopyrum species greatly enhance tolerance of recipient durum wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1378186. [PMID: 38766466 PMCID: PMC11099908 DOI: 10.3389/fpls.2024.1378186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/09/2024] [Indexed: 05/22/2024]
Abstract
Increased soil salinization, tightly related to global warming and drought and exacerbated by intensified irrigation supply, implies highly detrimental effects on staple food crops such as wheat. The situation is particularly alarming for durum wheat (DW), better adapted to arid/semi-arid environments yet more sensitive to salt stress than bread wheat (BW). To enhance DW salinity tolerance, we resorted to chromosomally engineered materials with introgressions from allied halophytic Thinopyrum species. "Primary" recombinant lines (RLs), having portions of their 7AL arms distally replaced by 7el1L Th. ponticum segments, and "secondary" RLs, harboring Th. elongatum 7EL insertions "nested" into 7el1L segments, in addition to near-isogenic lines lacking any alien segment (CLs), cv. Om Rabia (OR) as salt tolerant control, and BW introgression lines with either most of 7el1 or the complete 7E chromosome substitution as additional CLs, were subjected to moderate (100 mM) and intense (200 mM) salt (NaCl) stress at early growth stages. The applied stress altered cell cycle progression, determining a general increase of cells in G1 and a reduction in S phase. Assessment of morpho-physiological and biochemical traits overall showed that the presence of Thinopyrum spp. segments was associated with considerably increased salinity tolerance versus its absence. For relative water content, Na+ accumulation and K+ retention in roots and leaves, oxidative stress indicators (malondialdehyde and hydrogen peroxide) and antioxidant enzyme activities, the observed differences between stressed and unstressed RLs versus CLs was of similar magnitude in "primary" and "secondary" types, suggesting that tolerance factors might reside in defined 7el1L shared portion(s). Nonetheless, the incremental contribution of 7EL segments emerged in various instances, greatly mitigating the effects of salt stress on root and leaf growth and on the quantity of photosynthetic pigments, boosting accumulation of compatible solutes and minimizing the decrease of a powerful antioxidant like ascorbate. The seemingly synergistic effect of 7el1L + 7EL segments/genes made "secondary" RLs able to often exceed cv. OR and equal or better perform than BW lines. Thus, transfer of a suite of genes from halophytic germplasm by use of fine chromosome engineering strategies may well be the way forward to enhance salinity tolerance of glycophytes, even the sensitive DW.
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Affiliation(s)
- Sana Tounsi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sfax, Tunisia
| | - Debora Giorgi
- ENEA Casaccia Research Center, Department for Sustainability, Biotechnology and Agroindustry Division, Rome, Italy
| | - Ljiljana Kuzmanović
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Olfa Jrad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sfax, Tunisia
| | - Anna Farina
- ENEA Casaccia Research Center, Department for Sustainability, Biotechnology and Agroindustry Division, Rome, Italy
| | - Alessandra Capoccioni
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Rayda Ben Ayed
- Department of Agronomy and Plant Biotechnology, National Institute of Agronomy of Tunisia (INAT), University of Carthage, Tunis, Tunisia
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cédria, Hammam-lif, Tunisia
| | - Faiçal Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sfax, Tunisia
| | - Carla Ceoloni
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
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Wu N, He Z, Fang J, Liu X, Shen X, Zhang J, Lei Y, Xia Y, He H, Liu W, Chu C, Wang C, Qi Z. Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering. ANNALS OF BOTANY 2023; 131:185-198. [PMID: 35451455 PMCID: PMC9904354 DOI: 10.1093/aob/mcac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/20/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Dasypyrum villosum (2n = 2x = 14) harbours potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow the genetic base of wheat. A better solution is to utilize diversified D. villosum accessions as the genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information on the species. Using cytogenetic and molecular tools we analysed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat. METHODS A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. Polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content were used in genetic diversity analysis. KEY RESULTS Consensus karyotypes of D. villosum were developed, and the homoeologous statuses of individual D. villosum chromosomes relative to wheat were determined. Tandem repeat probes of pSc119.2, (GAA)10 and the AFA family produced high-resolution signals and not only showed different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids. CONCLUSIONS Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination (chromosome engineering), allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.
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Affiliation(s)
- Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziming He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaxin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhong Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yating Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Chenggen Chu
- USDA-ARS, Sugarbeet & Potato Research Unit, Fargo, ND 58102, USA
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Cápal P, Said M, Molnár I, Doležel J. Flow Cytometric Analysis and Sorting of Plant Chromosomes. Methods Mol Biol 2023; 2672:177-200. [PMID: 37335476 DOI: 10.1007/978-1-0716-3226-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Flow cytometry offers a unique way of analyzing and manipulating plant chromosomes. During a rapid movement in a liquid stream, large populations can be classified in a short time according to their fluorescence and light scatter properties. Chromosomes whose optical properties differ from other chromosomes in a karyotype can be purified by flow sorting and used in a range of applications in cytogenetics, molecular biology, genomics, and proteomics. As the samples for flow cytometry must be liquid suspensions of single particles, intact chromosomes must be released from mitotic cells. This protocol describes a procedure for preparation of suspensions of mitotic metaphase chromosomes from meristem root tips and their flow cytometric analysis and sorting for various downstream applications.
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Affiliation(s)
- Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, Giza, Cairo, Egypt
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
- Agricultural Institute, Centre for Agricultural Research, ELKH, Martonvásár, Hungary
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic.
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Zwyrtková J, Blavet N, Doležalová A, Cápal P, Said M, Molnár I, Vrána J, Doležel J, Hřibová E. Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. Int J Mol Sci 2022; 23:ijms23063191. [PMID: 35328613 PMCID: PMC8948999 DOI: 10.3390/ijms23063191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.
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Zhang S, Du P, Lu X, Fang J, Wang J, Chen X, Chen J, Wu H, Yang Y, Tsujimoto H, Chu C, Qi Z. Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat. Genome 2021; 65:205-217. [PMID: 34914567 DOI: 10.1139/gen-2021-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modern hexaploid wheat (Triticum aestivum L.; AABBDD) evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy played important roles in wheat evolution. How these variations occurred and their role in expanding the genetic diversity in modern wheat is mostly unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variation that occurs during the early generations of existence. SHW lines derived by crossing durum wheat 'Langdon' with twelve Ae. tauschii accessions were analyzed using oligonucelotide probe multiplex fluorescence in situ hybridization (FISH) to metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorized them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in SHW lines detected in this research may be an indication that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.
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Affiliation(s)
- Siyu Zhang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Pei Du
- Henan Academy of Agricultural Sciences, 74728, Henan Academy of Crop Molecular Breeding, Zhengzhou, Henan, China;
| | - Xueying Lu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaxin Fang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaqi Wang
- Nanjing Agricultural University, 70578, Weigang No.1, Nanjing, Jiangsu, China, 210095;
| | - Xuejun Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jianyong Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Hao Wu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Yang Yang
- Zaozhuang University, 372543, Zaozhuang, Shandong, China;
| | - Hisashi Tsujimoto
- Tottori University, 13114, Arid Land Research Center, Hamasaka, Tottori, Japan;
| | - Chenggen Chu
- USDA ARS, 17123, Fargo, North Dakota, United States;
| | - Zengjun Qi
- Nanjing Agricultural University, 70578, Weigang 1,Nanjing, Nanjing, China, 210095;
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Gao K, Zhou Y, Lu Q, Lu J, Su L, Su R, Zhang M, Tian Y, Wu L, Yan X. High-Throughput Human Telomere Length Analysis at the Single-Chromosome Level by FISH Coupled with Nano-Flow Cytometry. Anal Chem 2021; 93:9531-9540. [PMID: 34197088 DOI: 10.1021/acs.analchem.1c01544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Telomere length (TL) is a highly relevant biomarker for age-associated diseases and cancer, yet its clinical applications have been hindered by the inability of existing methods to rapidly measure the TL distribution and the percentage of chromosomes with critically short telomeres (CSTs, < 3 kb). Herein, we report the development of a high-throughput method to measure TL at the single-chromosome level. Metaphase chromosomes are isolated, hybridized with the Alexa Fluor 488-labeled telomeric peptide nucleic acid probe, and analyzed using a laboratory-built ultrasensitive nano-flow cytometer. The fluorescence intensity of individual chromosomes is converted to TL in kilobases upon external calibration. With an analysis rate of several thousand chromosomes per minute, a statistically robust TL distribution histogram is acquired in minutes, and the percentage of chromosomes with CSTs can be quickly assessed. By analyzing peripheral blood lymphocytes of 158 healthy donors, TL is found to shorten with age at a rate of 64 ± 3 bp/year and the percentage of chromosomes with CSTs increases with age at a rate of 0.32 ± 0.02%/year. Moreover, the data of 28 patients with chronic myeloid leukemia (CML) indicate that telomeres are significantly shorter at the time of diagnosis and the clinical phases of CML are closely associated with TL and the percentage of chromosomes with CSTs. This powerful tool could greatly deepen our understanding of telomere biology and improve the clinical utility of telomere biomarkers.
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Affiliation(s)
- Kaimin Gao
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yingxing Zhou
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Quanyi Lu
- Department of Hematology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen 361004, PR China
| | - Jingyuan Lu
- Department of Hematology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen 361004, PR China
| | - Liyun Su
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Rui Su
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, PR China
| | - Miaomiao Zhang
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Ye Tian
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Lina Wu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Xiaomei Yan
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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Doležel J, Lucretti S, Molnár I, Cápal P, Giorgi D. Chromosome analysis and sorting. Cytometry A 2021; 99:328-342. [PMID: 33615737 PMCID: PMC8048479 DOI: 10.1002/cyto.a.24324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow-sorted fractions, and their suitability for downstream applications.
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Affiliation(s)
- Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Sergio Lucretti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Debora Giorgi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
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Sartsanga C, Phengchat R, Fukui K, Wako T, Ohmido N. Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy. Chromosome Res 2021; 29:81-94. [PMID: 33615407 DOI: 10.1007/s10577-021-09649-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. This study aimed to develop a high-quality procedure for the isolation and preparation of plant chromosomes, maintaining the native chromosome structure, to elucidate the organization of chromatin fibers on the surface of plant chromosomes by electron microscopy. A simple technique to isolate intact barley (Hordeum vulgare) chromosomes with a high yield was developed, allowing chromosomes to be observed with a high-resolution scanning ion microscopy and helium ion microscopy (HIM) imaging technology, based on a scanning helium ion beam. HIM images from the surface chromatin fibers were analyzed to determine the size and alignment of the chromatin fibers. The unit size of the chromatin fibers was 11.6 ± 3.5 nm and was closely aligned to the chromatin network model. Our findings indicate that compacting the surface structure of barley via a chromatin network and observation via HIM are powerful tools for investigating the structure of chromatin.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan.
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Zwyrtková J, Šimková H, Doležel J. Chromosome genomics uncovers plant genome organization and function. Biotechnol Adv 2020; 46:107659. [PMID: 33259907 DOI: 10.1016/j.biotechadv.2020.107659] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
The identification of causal genomic loci and their interactions underlying various traits in plants has been greatly aided by progress in understanding the organization of the nuclear genome. This provides clues to the responses of plants to environmental stimuli at the molecular level. Apart from other uses, these insights are needed to fully explore the potential of new breeding techniques that rely on genome editing. However, genome analysis and sequencing is not straightforward in the many agricultural crops and their wild relatives that possess large and complex genomes. Chromosome genomics streamlines this task by dissecting the genome to single chromosomes whose DNA is then used instead of nuclear DNA. This results in a massive and lossless reduction in DNA sample complexity, reduces the time and cost of the experiment, and simplifies data interpretation. Flow cytometric sorting of condensed mitotic chromosomes makes it possible to purify single chromosomes in large quantities, and as the DNA remains intact this process can be coupled successfully with many techniques in molecular biology and genomics. Since the first experiments with flow cytometric sorting in the late 1980s, numerous applications have been developed, and chromosome genomics has been having a significant impact in many areas of research, including the sequencing of complex genomes of important crops and gene cloning. This review discusses these applications, describes their contribution to advancements in plant genome analysis and gene cloning, and outlines future directions.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
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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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Němečková A, Wäsch C, Schubert V, Ishii T, Hřibová E, Houben A. CRISPR/Cas9-Based RGEN-ISL Allows the Simultaneous and Specific Visualization of Proteins, DNA Repeats, and Sites of DNA Replication. Cytogenet Genome Res 2019; 159:48-53. [PMID: 31610539 DOI: 10.1159/000502600] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2019] [Indexed: 11/19/2022] Open
Abstract
Visualizing the spatiotemporal organization of the genome will improve our understanding of how chromatin structure and function are intertwined. Here, we describe a further development of the CRISPR/Cas9-based RNA-guided endonuclease-in situ labeling (RGEN-ISL) method. RGEN-ISL allowed the differentiation between vertebrate-type (TTAGGG)n and Arabidopsis-type (TTTAGGG)n telomere repeats. Using maize as an example, we established a combination of RGEN-ISL, immunostaining, and EdU labeling to visualize in situ specific repeats, histone marks, and DNA replication sites, respectively. The effects of the non-denaturing RGEN-ISL and standard denaturing FISH on the chromatin structure were compared using super-resolution microscopy. 3D structured illumination microscopy revealed that denaturation and acetic acid fixation impaired and flattened the chromatin. The broad range of adaptability of RGEN-ISL to different combinations of methods has the potential to advance the field of chromosome biology.
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Zhang S, Zhu M, Shang Y, Wang J, Dawadundup, Zhuang L, Zhang J, Chu C, Qi Z. Physical organization of repetitive sequences and chromosome diversity of barley revealed by fluorescence in situ hybridization (FISH). Genome 2019; 62:329-339. [PMID: 30933665 DOI: 10.1139/gen-2018-0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fluorescence in situ hybridization (FISH) using oligonucleotides is a simple and convenient method for chromosome research. In this study, 34 of 46 previously developed oligonucleotides produced signals in barley. Together with two plasmid clones and one PCR-amplified cereal centromere repeat (CCS1) probe, 37 repetitive sequences were chromosomally located produced three types of signals covering different positions on the chromosomes. The centromeric and pericentric regions had a more complex genomic organization and sequence composition probably indicative of higher contents of heterochromatin. An efficient multi-plex probe containing eight oligonucleotides and a plasmid clone of 45S rDNA was developed. Thirty-three barley karyotypes were developed and compared. Among them, 11 irradiation-induced mutants of cultivar 08-49 showed no chromosomal variation, whereas 22 cultivar and landrace accessions contained 28 chromosomal polymorphisms. Chromosome 4H was the most variable and 6H was the least variable based on chromosome polymorphic information content (CPIC). Five polymorphic chromosomes (1H-2, 2H-1, 3H-3, 5H-2, and 6H-2) were dominant types, each occurring in more than 50% of accessions. The multi-plex probe should facilitate identification of further chromosomal polymorphisms in barley.
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Affiliation(s)
- Siyu Zhang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Minqiu Zhu
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.,b Changshu Institute of Technology, Changshu 215500, Jiangsu, China
| | - Yi Shang
- c Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China.,d Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, China
| | - Jiaqi Wang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dawadundup
- e Institute of Agriculture, Tibet Academy of Agricultural and Animal Science, Lhasa 850032, China
| | - Lifang Zhuang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlong Zhang
- f Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Chenggen Chu
- g Texas A&M Agrilife Research, Amarillo, TX 79106, USA
| | - Zengjun Qi
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Sattler MC, Soares FAF, Silva JC, Carvalho CR, Clarindo WR. Physical Mapping of 5S rDNA in Eucalyptus dunnii Maiden and Zea mays L. by PRINS. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
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15
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Huang X, Zhu M, Zhuang L, Zhang S, Wang J, Chen X, Wang D, Chen J, Bao Y, Guo J, Zhang J, Feng Y, Chu C, Du P, Qi Z, Wang H, Chen P. Structural chromosome rearrangements and polymorphisms identified in Chinese wheat cultivars by high-resolution multiplex oligonucleotide FISH. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1967-1986. [PMID: 29947816 DOI: 10.1007/s00122-018-3126-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/01/2018] [Indexed: 05/02/2023]
Abstract
High-resolution multiplex oligonucleotide FISH revealed the frequent occurrence of structural chromosomal rearrangements and polymorphisms in widely grown wheat cultivars and their founders. Over 2000 wheat cultivars including 19 founders were released and grown in China from 1949 to 2000. To understand the impact of breeding selection on chromosome structural variations, high-resolution karyotypes of Chinese Spring (CS) and 373 Chinese cultivars were developed and compared by FISH (fluorescence in situ hybridization) using an oligonucleotide multiplex probe based on repeat sequences. Among them, 148 (39.7%) accessions carried 14 structural rearrangements including three single translocations (designated as T), eight reciprocal translocations (RT), one pericentric inversion (perInv), and two combined variations having both the deletion and single translocations. Five rearrangements were traced to eight founders, including perInv 6B detected in 57 cultivars originating from Funo, Abbondanza, and Fan 6, T 1RS∙1BL in 47 cultivars derived from the Lovrin series, RT 4AS∙4AL-1DS/1DL∙1DS-4AL in 31 varieties from Mazhamai and Bima 4, RT 1RS∙7DL/7DS∙1BL in three cultivars was from Aimengniu, and RT 5BS∙5BL-5DL/5DS∙5DL-5BL was only detected in Youzimai. In addition to structural rearrangements, 167 polymorphic chromosome blocks (defined as unique signal patterns of oligonucleotide repeat probes distributed within chromosomes) were identified, and 59 were present in one or more founders. Some specific types were present at high frequencies indicating selective blocks in Chinese wheat varieties. All cultivars and CS were clustered into four groups and 15 subgroups at chromosome level. Common block patterns occurred in the same subgroup. Origin, geographic distribution, probable adaptation to specific environments, and potential use of these chromosomal rearrangements and blocks are discussed.
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Affiliation(s)
- Xinyi Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minqiu Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lifang Zhuang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siyu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuejun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danrui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianyong Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, 271018, China
| | - Jie Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jinlong Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Yigao Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenggen Chu
- Texas A&M Agrilife Research, Amarillo, TX, 79106, USA
| | - Pei Du
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, 271018, China.
| | - Peidu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Moreno R, Castro P, Vrána J, Kubaláková M, Cápal P, García V, Gil J, Millán T, Doležel J. Integration of Genetic and Cytogenetic Maps and Identification of Sex Chromosome in Garden Asparagus ( Asparagus officinalis L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1068. [PMID: 30108600 PMCID: PMC6079222 DOI: 10.3389/fpls.2018.01068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/02/2018] [Indexed: 05/30/2023]
Abstract
A genetic linkage map of dioecious garden asparagus (Asparagus officinalis L., 2n = 2x = 20) was constructed using F1 population, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. In total, 1376 SNPs and 27 SSRs were used for genetic mapping. Two resulting parental maps contained 907 and 678 markers spanning 1947 and 1814 cM, for female and male parent, respectively, over ten linkage groups representing ten haploid chromosomes of the species. With the aim to anchor the ten genetic linkage groups to individual chromosomes and develop a tool to facilitate genome analysis and gene cloning, we have optimized a protocol for flow cytometric chromosome analysis and sorting in asparagus. The analysis of DAPI-stained suspensions of intact mitotic chromosomes by flow cytometry resulted in histograms of relative fluorescence intensity (flow karyotypes) comprising eight major peaks. The analysis of chromosome morphology and localization of 5S and 45S rDNA by FISH on flow-sorted chromosomes, revealed that four chromosomes (IV, V, VI, VIII) could be discriminated and sorted. Seventy-two SSR markers were used to characterize chromosome content of individual peaks on the flow karyotype. Out of them, 27 were included in the genetic linkage map and anchored genetic linkage groups to chromosomes. The sex determining locus was located on LG5, which was associated with peak V representing a chromosome with 5S rDNA locus. The results obtained in this study will support asparagus improvement by facilitating targeted marker development and gene isolation using flow-sorted chromosomes.
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Affiliation(s)
- Roberto Moreno
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Patricia Castro
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Verónica García
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Juan Gil
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Teresa Millán
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Koba T. An improved method for inducing prometaphase chromosomes in plants. Mol Cytogenet 2018; 11:32. [PMID: 29760782 PMCID: PMC5946395 DOI: 10.1186/s13039-018-0380-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/23/2018] [Indexed: 01/14/2023] Open
Abstract
Background Detailed karyotyping using metaphase chromosomes in melon (Cucumis melo L.) remains a challenge because of their small chromosome sizes and poor stainability. Prometaphase chromosomes, which are two times longer and loosely condensed, provide a significantly better resolution for fluorescence in situ hybridization (FISH) than metaphase chromosomes. However, suitable method for acquiring prometaphase chromosomes in melon have been poorly investigated. Results In this study, a modified Carnoy’s solution II (MC II) [6:3:1 (v/v) ethanol: acetic acid: chloroform] was used as a pretreatment solution to obtain prometaphase chromosomes. We demonstrated that the prometaphase chromosomes obtained using the MC II method are excellent for karyotyping and FISH analysis. We also observed that a combination of MC II and the modified air dry (ADI) method provides a satisfactory meiotic pachytene chromosome preparation with reduced cytoplasmic background and clear chromatin spreads. Moreover, we demonstrated that pachytene and prometaphase chromosomes of melon and Abelia × grandiflora generate significantly better FISH images when prepared using the method described. We confirmed, for the first time, that Abelia × grandiflora has pairs of both strong and weak 45S ribosomal DNA signals on the short arms of their metaphase chromosomes. Conclusion The MC II and ADI method are simple and effective for acquiring prometaphase and pachytene chromosomes with reduced cytoplasm background in plants. Our methods provide high-resolution FISH images that can help accelerate molecular cytogenetic research in plants.
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Affiliation(s)
- Agus Budi Setiawan
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Chee How Teo
- 2Center for Research in Biotechnology for Agriculture, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shinji Kikuchi
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Hidenori Sassa
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Takato Koba
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
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Bačovský V, Hobza R, Vyskot B. Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes. Methods Mol Biol 2018; 1675:509-535. [PMID: 29052211 DOI: 10.1007/978-1-4939-7318-7_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
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Affiliation(s)
- Václaclav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
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19
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Rodrigues ASB, Silva SE, Pina-Martins F, Loureiro J, Castro M, Gharbi K, Johnson KP, Dietrich CH, Borges PAV, Quartau JA, Jiggins CD, Paulo OS, Seabra SG. Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources. BMC Genet 2016; 17:144. [PMID: 27846816 PMCID: PMC5111214 DOI: 10.1186/s12863-016-0455-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0455-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana S B Rodrigues
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.
| | - Sara E Silva
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.,Centro de Estudos do Ambiente e do Mar (CESAM), DBA/FCUL, Lisbon, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Paulo A V Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências e Engenharia do Ambiente, Angra do Heroísmo, Açores, Portugal
| | - José A Quartau
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
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20
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Detection of Changes in the Medicago sativa Retinoblastoma-Related Protein (MsRBR1) Phosphorylation During Cell Cycle Progression in Synchronized Cell Suspension Culture. Methods Mol Biol 2016. [PMID: 27815909 DOI: 10.1007/978-1-4939-6603-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Deepening our knowledge on the regulation of the plant cell division cycle depends on techniques that allow for the enrichment of cell populations in defined cell cycle phases. Synchronization of cell division can be achieved using different plant tissues; however, well-established cell suspension cultures provide large amount of biological sample for further analyses. Here, we describe the methodology of the establishment, propagation, and analysis of a Medicago sativa suspension culture that can be used for efficient synchronization of the cell division. A novel 5-ethynyl-2'-deoxyuridine (EdU)-based method is used for the estimation of cell fraction that enters DNA synthesis phase of the cell cycle and we also demonstrate the changes in the phosphorylation level of Medicago sativa retinoblastoma-related protein (MsRBR1) during cell cycle progression.
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Molnár I, Vrána J, Burešová V, Cápal P, Farkas A, Darkó É, Cseh A, Kubaláková M, Molnár-Láng M, Doležel J. Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:452-467. [PMID: 27402341 DOI: 10.1111/tpj.13266] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/09/2023]
Abstract
Goat grasses (Aegilops spp.) contributed to the evolution of bread wheat and are important sources of genes and alleles for modern wheat improvement. However, their use in alien introgression breeding is hindered by poor knowledge of their genome structure and a lack of molecular tools. The analysis of large and complex genomes may be simplified by dissecting them into single chromosomes via flow cytometric sorting. In some species this is not possible due to similarities in relative DNA content among chromosomes within a karyotype. This work describes the distribution of GAA and ACG microsatellite repeats on chromosomes of the U, M, S and C genomes of Aegilops, and the use of microsatellite probes to label the chromosomes in suspension by fluorescence in situ hybridization (FISHIS). Bivariate flow cytometric analysis of chromosome DAPI fluorescence and fluorescence of FITC-labelled microsatellites made it possible to discriminate all chromosomes and sort them with negligible contamination by other chromosomes. DNA of purified chromosomes was used as a template for polymerase chain reation (PCR) using Conserved Orthologous Set (COS) markers with known positions on wheat A, B and D genomes. Wheat-Aegilops macrosyntenic comparisons using COS markers revealed significant rearrangements in the U and C genomes, while the M and S genomes exhibited structure similar to wheat. Purified chromosome fractions provided an attractive resource to investigate the structure and evolution of the Aegilops genomes, and the COS markers assigned to Aegilops chromosomes will facilitate alien gene introgression into wheat.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Veronika Burešová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
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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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Abstract
Good preparations are essential for informative analysis of both somatic and meiotic chromosomes, cytogenetics, and cell divisions. Fluorescent chromosome staining allows even small chromosomes to be visualized and counted, showing their morphology. Aneuploidies and polyploidies can be established for species, populations, or individuals while changes occurring in breeding lines during hybridization or tissue culture and transformation protocols can be assessed. The process of division can be followed during mitosis and meiosis including pairing and chiasma distribution, as well as DNA organization and structure during the evolution of chromosomes can be studied. This chapter presents protocols for pretreatment and fixation of material, including tips of how to grow plants to get good and healthy meristem with many divisions. The chromosome preparation technique is described using proteolytic enzymes, but acids can be used instead. Chromosome slide preparations are suitable for fluorochrome staining for fast screening (described in the chapter) or fluorescent in situ hybridization (see Schwarzacher and Heslop-Harrison, In situ hybridization. BIOS Scientific Publishers, Oxford, 2000).
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Affiliation(s)
- Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Vrána J, Cápal P, Číhalíková J, Kubaláková M, Doležel J. Flow Sorting Plant Chromosomes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2016. [PMID: 27511171 DOI: 10.1023/a:1024322001786] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic.
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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Abstract
Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic.
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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Cell synchronization and isolation of chromosomes from Chinese fir root tips for flow cytometric analysis. Biotechnol Lett 2015; 37:1309-14. [DOI: 10.1007/s10529-015-1800-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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Escudero M, Maguilla E, Loureiro J, Castro M, Castro S, Luceño M. Genome size stability despite high chromosome number variation in Carex gr. laevigata. AMERICAN JOURNAL OF BOTANY 2015; 102:233-8. [PMID: 25667076 DOI: 10.3732/ajb.1400433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY In organisms with holocentric chromosomes like Carex species, chromosome number evolution has been hypothesized to be a result of fission, fusion, and/or translocation events. Negative, positive, or the absence of correlations have been found between chromosome number and genome size in Carex. METHODS Using the inferred diploid chromosome number and 80 genome size measurements from 26 individuals and 20 populations of Carex gr. laevigata, we tested the null hypothesis of chromosome number evolution by duplication and deletion of whole chromosomes. KEY RESULTS Our results show a significant positive correlation between genome size and chromosome number, but the slope of such correlation supports the hypothesis of proliferation and removal of repetitive DNA fragments to explain genome size variation rather than duplication and deletion of whole chromosomes. CONCLUSIONS Our results refine the theory of the holokinetic drive: this mechanism is proposed to facilitate repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited, or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. This study sheds light on how karyotype evolution plays an important role in the diversification of the species of the genus Carex.
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Affiliation(s)
- Marcial Escudero
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Americo Vespucio sn 41092 Seville, Spain
| | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Carretera de Utrera Km 1 sn 41013 Seville, Spain
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Modesto Luceño
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Carretera de Utrera Km 1 sn 41013 Seville, Spain
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Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A. LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Res 2014; 22:91-100. [PMID: 25428895 PMCID: PMC4379980 DOI: 10.1093/dnares/dsu042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
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Affiliation(s)
- Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Tommaso Giordani
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Rosa Maria Cossu
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Michele Morgante
- Department of Crop and Environmental Sciences, University of Udine, Udine, Italy Institute of Applied Genomics, Udine, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
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Crosby K, Stokes TO, Latta RG. Evolving California genotypes of Avena barbata are derived from multiple introductions but still maintain substantial population structure. PeerJ 2014; 2:e633. [PMID: 25392753 PMCID: PMC4226642 DOI: 10.7717/peerj.633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/01/2014] [Indexed: 11/21/2022] Open
Abstract
Multiple introductions are thought to enhance the chance of successful colonization, in part because recombination may generate adaptive variation to a new environment. Avena barbata (slender wild oat) is a successful colonist in California, historically noted for striking genetic divergence into two multilocus genotypes, but is still undergoing adaptive change. We sought to understand whether multiple introductions might be contributing to this change. We used cpDNA phylogeography of A. barbata within its home range and in its invaded range in California to determine the minimum number of separate introductions, and the spatial distribution of these introduced lineages. We collected from sites throughout the state of California, where it is an invasive species. Accessions from a representative portion of A. barbata’s full native range were obtained from germplasm repositories. We sequenced seven intergenic chloroplast DNA loci for A. barbata individuals both in California (novel geographic range) and its ancestral range. 204 individuals were assayed for chloroplast haplotype within California using single strand conformational polymorphism SSCPs. Genome size was determined by flow cytometry. Californian accessions are tetraploid as expected, but their genome sizes were smaller than the Old World accessions. There were three haplotypes present in California that were identical to haplotypes in the native range. Within California, the presence of multiple haplotypes at a site was observed primarily in Northern and Central populations. Between populations there was still substantial structure with FST ∼ 0.33, due to a shallow latitudinal cline caused by a preponderance of xeric haplotypes in Southern California. There was a minimum of three seed introductions to California. Recombination is thus likely to occur, and contribute to adaptation in new range in this highly-selfing, invader.
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Affiliation(s)
- Kate Crosby
- Department of Biology, Dalhousie University , Halifax, NS , Canada
| | - Taylor O Stokes
- Department of Biology, Dalhousie University , Halifax, NS , Canada
| | - Robert G Latta
- Department of Biology, Dalhousie University , Halifax, NS , Canada
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31
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Petrovská B, Jeřábková H, Chamrád I, Vrána J, Lenobel R, Uřinovská J, Šebela M, Doležel J. Proteomic Analysis of Barley Cell Nuclei Purified by Flow Sorting. Cytogenet Genome Res 2014; 143:78-86. [DOI: 10.1159/000365311] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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32
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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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Grosso V, Farina A, Gennaro A, Giorgi D, Lucretti S. Flow sorting and molecular cytogenetic identification of individual chromosomes of Dasypyrum villosum L. (H. villosa) by a single DNA probe. PLoS One 2012; 7:e50151. [PMID: 23185561 PMCID: PMC3502404 DOI: 10.1371/journal.pone.0050151] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/19/2012] [Indexed: 11/19/2022] Open
Abstract
Dasypyrum villosum (L.) Candargy (sin. Haynaldia villosa) is an annual wild diploid grass species (2n = 2x = 14; genome VV) belonging to the Poaceae family, which is considered to be an important source of biotic and abiotic stress resistance genes for wheat breeding. Enhanced characterization of D. villosum chromosomes can facilitate exploitation of its gene pool and its use in wheat breeding programs. Here we present the cytogenetic identification of D. villosum chromosomes on slide by fluorescent in situ hybridization (FISH), with the GAA simple sequence repeat (SSR) as a probe. We also describe the isolation and the flow cytometric analysis of D. villosum chromosomes in suspension, resulting in a distinguished flow karyotype. Chromosomes were flow sorted into three fractions, according their DNA content, one of which was composed of a single type of chromosome, namely 6 V, sorted with over 85% purity. Chromosome 6 V is known to carry genes to code for important resistance and seed storage characteristics, and its isolation represents a new source of genetic traits and specific markers useful for wheat improvement.
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Affiliation(s)
| | | | - Andrea Gennaro
- Department of Agriculture, Forestry, Nature and Energy - DAFNE, University of Tuscia, Viterbo, Italy
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35
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Lee JH, Arumuganathan K, Kaeppler SM, Papa CM, Kaeppler HF. Cell synchronization and isolation of metaphase chromosomes from maize (Zea mays L.) root tips for flow cytometric analysis and sorting. Genome 2012; 39:697-703. [PMID: 18469929 DOI: 10.1139/g96-088] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Accumulation of cells containing metaphase chromosomes is an important step in cytological analyses and chromosome sorting procedures. The goal of this research was to optimize treatment parameters to synchronize the cell cycle of maize root tip meristem cells. Levels of hydroxyurea, a DNA synthesis inhibitor, were assessed for their utility in accumulating cells at the G1 phase of the cell cycle. Trifluralin, amiprophos-methyl, and colchicine were used to accumulate cells containing metaphase chromosomes upon release from hydroxyurea inhibition. Optimal mitotic indices were achieved by treating seedlings with 5 mM hydroxyurea for 18 h, incubating for 1 h without chemical treatment to release the hydroxyurea block, and then treating emerging roots with 1 μM trifluralin for 4 h. The mitotic index of synchronized maize root tips was over 70%. Uniformity of synchronization depended upon selection of seeds with emerging radicles that were similar in length at the time of treatment. Suspensions of intact chromosomes were prepared by a simple slicing procedure. The chromosome preparations were found to be suitable for flow cytometric characterization and sorting. Chromosome peaks of the observed flow karyotype resembled the predicted flow karyotype calculated on the basis of maize chromosome size. Key words : flow karyotype, hydroxyurea, plant chromosome sorting, trifluralin.
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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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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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Molnár I, Kubaláková M, Šimková H, Cseh A, Molnár-Láng M, Doležel J. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata. PLoS One 2011; 6:e27708. [PMID: 22132127 PMCID: PMC3223179 DOI: 10.1371/journal.pone.0027708] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 10/22/2011] [Indexed: 01/20/2023] Open
Abstract
This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.
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Affiliation(s)
- István Molnár
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - András Cseh
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Márta Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
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39
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Tisi A, Federico R, Moreno S, Lucretti S, Moschou PN, Roubelakis-Angelakis KA, Angelini R, Cona A. Perturbation of polyamine catabolism can strongly affect root development and xylem differentiation. PLANT PHYSIOLOGY 2011; 157:200-15. [PMID: 21746808 PMCID: PMC3165870 DOI: 10.1104/pp.111.173153] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 07/11/2011] [Indexed: 05/02/2023]
Abstract
Spermidine (Spd) treatment inhibited root cell elongation, promoted deposition of phenolics in cell walls of rhizodermis, xylem elements, and vascular parenchyma, and resulted in a higher number of cells resting in G(1) and G(2) phases in the maize (Zea mays) primary root apex. Furthermore, Spd treatment induced nuclear condensation and DNA fragmentation as well as precocious differentiation and cell death in both early metaxylem and late metaxylem precursors. Treatment with either N-prenylagmatine, a selective inhibitor of polyamine oxidase (PAO) enzyme activity, or N,N(1)-dimethylthiourea, a hydrogen peroxide (H(2)O(2)) scavenger, reverted Spd-induced autofluorescence intensification, DNA fragmentation, inhibition of root cell elongation, as well as reduction of percentage of nuclei in S phase. Transmission electron microscopy showed that N-prenylagmatine inhibited the differentiation of the secondary wall of early and late metaxylem elements, and xylem parenchymal cells. Moreover, although root growth and xylem differentiation in antisense PAO tobacco (Nicotiana tabacum) plants were unaltered, overexpression of maize PAO (S-ZmPAO) as well as down-regulation of the gene encoding S-adenosyl-l-methionine decarboxylase via RNAi in tobacco plants promoted vascular cell differentiation and induced programmed cell death in root cap cells. Furthermore, following Spd treatment in maize and ZmPAO overexpression in tobacco, the in vivo H(2)O(2) production was enhanced in xylem tissues. Overall, our results suggest that, after Spd supply or PAO overexpression, H(2)O(2) derived from polyamine catabolism behaves as a signal for secondary wall deposition and for induction of developmental programmed cell death.
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Affiliation(s)
| | | | | | | | | | | | | | - Alessandra Cona
- Department of Biology, University Roma Tre, 00146 Rome, Italy (A.T., R.F., S.M., R.A., A.C.); ENEA Casaccia Research Center, BIOTEC GEN, 00123 Rome, Italy (S.L.); and Department of Biology, University of Crete, 71409 Heraklion, Greece (P.N.M., K.A.R.-A.)
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40
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Ayaydin F, Kotogány E, Abrahám E, Horváth GV. Synchronization of Medicago sativa cell suspension culture. Methods Mol Biol 2011; 761:227-38. [PMID: 21755452 DOI: 10.1007/978-1-61779-182-6_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Deepening our knowledge on the regulation of the plant cell division cycle depends on techniques that allow for the enrichment of cell populations in defined cell cycle phases. Synchronization of cell division can be achieved using different plant tissues; however, well-established cell suspension cultures provide the largest amount of biological sample for further analysis. Here we describe the methodology of the establishment, propagation, and analysis of a Medicago sativa suspension culture that can be used for efficient synchronization of the cell division and also the application and removal of hydroxyurea blocking agent. A novel method is used for the estimation of cell portion that enters S phase during the assay. The protocol can be used in the case of other species as well.
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Affiliation(s)
- Ferhan Ayaydin
- Cellular Imaging Laboratory, Biological Research Centre, Hungarian Academy of Sciences, H-6726, Szeged, Temesvárt krt. 62, Hungary.
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41
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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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42
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Gemperlová L, Cvikrová M, Fischerová L, Binarová P, Fischer L, Eder J. Polyamine metabolism during the cell cycle of synchronized tobacco BY-2 cell line. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:584-91. [PMID: 19321355 DOI: 10.1016/j.plaphy.2009.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 02/23/2009] [Accepted: 02/28/2009] [Indexed: 05/27/2023]
Abstract
The time courses of the contents of free, soluble and insoluble polyamine (PA) conjugates, PA biosynthetic and catabolic enzyme activities and mRNA levels of PA biosynthetic genes were monitored during the cell cycle of synchronized tobacco BY-2 cell line (Nicotiana tabacum L. cv. Bright Yellow 2). Progression through the cell cycle was characterized by specific biphasic changes of PA levels. The first, moderate peak in the amount of free PAs coincided with the S-phase. After a transient decline in G2 phase the contents of free PAs increased rapidly and peaked again during G2/M interface. Then sharply decreased with the minimum at the end of mitosis and during M/G1 transition and started to rise again with the next replication phase. Levels of PA soluble conjugates paralleled those of the free forms. Biosynthetic enzyme activities followed the biphasic manner analogous to the levels of free PAs and seemed to be regulated on both transcriptional and (post)translational level. PA cellular levels were further controlled by both catabolic degradation and conjugation of PAs. PA catabolism played an important role in the PA down-regulation during G2 phase and late mitosis, while the decline in free PAs in G2/M interface and during the whole mitosis resulted mainly from PA conjugation. This study's results demonstrate that during the cell cycle of tobacco BY-2 cells endogenous PA levels are intricately controlled, involving regulation of activities of biosynthetic, catabolic and conjugation enzymes.
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Affiliation(s)
- Lenka Gemperlová
- Institute of Experimental Botany v.v.i., Academy of Sciences of the Czech Republic, Rozvojová 236, 16502 Prague 6, Czech Republic
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43
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Dolezel J, Macas J, Lucretti S. Flow analysis and sorting of plant chromosomes. CURRENT PROTOCOLS IN CYTOMETRY 2008; Chapter 5:Unit 5.3. [PMID: 18770713 DOI: 10.1002/0471142956.cy0503s09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of flow cytometry for evaluation of plant chromosomes requires some specialized attention to preparation and instrumentation. This unit deals exclusively with plant cytogenetics and presents an outline of this area as well as methods for accumulation of cells in metaphase, preparation of chromosome suspensions, flow analysis and sorting of chromosomes, and processing of the sorted chromosomes. Each method is described in tremendous detail because in many aspects dealing with plant cells is quite different from dealing with mammalian cells. Supporting histograms are presented as well as a range of special hints on dealing with plant material and a discussion of the utility of sorted chromosomes for plant genome mapping.
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Affiliation(s)
- J Dolezel
- Institute of Experimental Botany, Olomouc, Czech Republic
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44
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Cvikrová M, Gemperlová L, Eder J, Zazímalová E. Excretion of polyamines in alfalfa and tobacco suspension-cultured cells and its possible role in maintenance of intracellular polyamine contents. PLANT CELL REPORTS 2008; 27:1147-56. [PMID: 18369627 DOI: 10.1007/s00299-008-0538-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 03/06/2008] [Indexed: 05/26/2023]
Abstract
Changes in polyamines (PAs) in cells and cultivation media of alfalfa (Medicago sativa L.) and tobacco bright yellow 2 (BY-2) (Nicotiana tabacum L.) cell suspension cultures were studied over their growth cycles. The total content of PAs (both free and conjugated forms) was nearly 10 times higher in alfalfa, with high level of free putrescine (Put) (in exponential growth phase it represented about 65-73% of the intracellular Put pool). In contrast, the high content of soluble Put conjugates was found in tobacco cells (in exponential phase about 70% of the intracellular Put). Marked differences occurred in the amount of PAs excreted into the cultivation medium: alfalfa cells excreted at the first day after inoculation 2117.0, 230.5, 29.0 and 88.0 nmol g(-1) of cell fresh weight (FW) of Put, spermidine (Spd), spermine (Spm) and cadaverine (Cad), respectively, while at the same time tobacco cells excreted only small amount of Put and Spd (12.7 and 2.4 nmol g(-1) FW, respectively). On day 1 the amounts of Put, Spd, Spm and Cad excreted by alfalfa cells represented 21, 38, 12 and 15% of the total pool (intra- plus extra-cellular contents) of Put, Spd, Spm and Cad, respectively. In the course of lag-phase and the beginning of exponential phase the relative contents of extracellular PAs continually decreased (with the exception of Cad). On day 10, the extracellular Put, Spd, Spm and Cad still represented 11.3, 10.9, 2.1 and 27% of their total pools. The extracellular PAs in tobacco cells represented from day 3 only 0.1% from their total pools. The possible role of PA excretion into the cultivation medium in maintenance of intracellular PA contents in the cells of the two cell culture systems, differing markedly in growth rate and PA metabolism is discussed.
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Affiliation(s)
- Milena Cvikrová
- Institute of Experimental Botany v.v.i, Academy of Sciences of the Czech Republic, Rozvojová 236, 16502 Prague 6, Czech Republic.
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45
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Kasprzak A, Šafář J, Janda J, Doležel J, Wolko B, Naganowska B. The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.). Cell Mol Biol Lett 2007; 11:396-407. [PMID: 16847554 PMCID: PMC6472840 DOI: 10.2478/s11658-006-0033-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 05/30/2006] [Indexed: 11/20/2022] Open
Abstract
The narrow-leafed lupin possesses valuable traits for environment-friendly agriculture and for the production of unconventional agricultural products. Despite various genetic and environmental studies, the breeding of improved cultivars has been slow due to the limited knowledge of its genomic structure. Further advances in genomics require, among other things, the availability of a genomic DNA library with large inserts. We report here on the construction of the first DNA library cloned in a BAC (bacterial artificial chromosome) vector from diploid Lupinus angustifolius L. cv. Sonet. The high molecular weight DNA used for its preparation was isolated from interphase nuclei that were purified by flow cytometry. The library comprises 55,296 clones and is ordered in 144x384-well microtitre plates. With an average insert size of 100 kb, the library represents six haploid genome equivalents. Thanks to the purification of the nuclei by flow cytometry, contamination with chloroplast DNA and mitochondrial DNA was negligible. The availability of a BAC library opens avenues for the development of a physical contig map and positional gene cloning, as well as for the analysis of the plant's genome structure and evolution.
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Affiliation(s)
- Andrzej Kasprzak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Jan Šafář
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Sokolovská 6, CZ-772 00 Olomouc, Czech Republic
| | - Jaroslav Janda
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Sokolovská 6, CZ-772 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Sokolovská 6, CZ-772 00 Olomouc, Czech Republic
| | - Bogdan Wolko
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
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46
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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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47
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Spíchal L, Krystof V, Paprskárová M, Lenobel R, Styskala J, Binarová P, Cenklová V, De Veylder L, Inzé D, Kontopidis G, Fischer PM, Schmülling T, Strnad M. Classical Anticytokinins Do Not Interact with Cytokinin Receptors but Inhibit Cyclin-dependent Kinases. J Biol Chem 2007; 282:14356-63. [PMID: 17339323 DOI: 10.1074/jbc.m609750200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytokinins are a class of plant hormones that regulate the cell cycle and diverse developmental and physiological processes. Several compounds have been identified that antagonize the effects of cytokinins. Based on structural similarities and competitive inhibition, it has been assumed that these anticytokinins act through a common cellular target, namely the cytokinin receptor. Here, we examined directly the possibility that various representative classical anticytokinins inhibit the Arabidopsis cytokinin receptors CRE1/AHK4 (cytokinin response 1/Arabidopsis histidine kinase 4) and AHK3 (Arabidopsis histidine kinase 3). We show that pyrrolo[2,3-d]pyrimidine and pyrazolo[4,3-d]pyrimidine anticytokinins do not act as competitors of cytokinins at the receptor level. Flow cytometry and microscopic analyses revealed that anticytokinins inhibit the cell cycle and cause disorganization of the microtubular cytoskeleton and apoptosis. This is consistent with the hypothesis that they inhibit regulatory cyclin-dependent kinase (CDK) enzymes. Biochemical studies demonstrated inhibition by selected anti-cytokinins of both Arabidopsis and human CDKs. X-ray determination of the crystal structure of a human CDK2-anticytokinin complex demonstrated that the antagonist occupies the ATP-binding site of CDK2. Finally, treatment of human cancer cell lines with anticytokinins demonstrated their ability to kill human cells with similar effectiveness as known CDK inhibitors.
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MESH Headings
- Apoptosis
- Arabidopsis/metabolism
- Arabidopsis Proteins/metabolism
- Bone Neoplasms/metabolism
- Bone Neoplasms/pathology
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carrier Proteins
- Cell Cycle
- Cell Proliferation/drug effects
- Crystallography, X-Ray
- Cyclin-Dependent Kinase 2/antagonists & inhibitors
- Cyclin-Dependent Kinase 2/metabolism
- Cytokinins/antagonists & inhibitors
- Cytokinins/metabolism
- Cytoskeleton
- Flow Cytometry
- Gene Expression Regulation, Plant
- Histidine Kinase
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Osteosarcoma/metabolism
- Osteosarcoma/pathology
- Protein Kinases/metabolism
- Pyrimidines/pharmacology
- Receptors, Cell Surface/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Lukás Spíchal
- Laboratory of Growth Regulators, Institute of Experimental Botany, AS CR and Palacký University, Slechtitelů 11, Olomouc, Czech Republic
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48
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Affiliation(s)
- David W Galbraith
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
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49
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Kubaláková M, Valárik M, Barto J, Vrána J, Cíhalíková J, Molnár-Láng M, Dolezel J. Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 2004; 46:893-905. [PMID: 14608406 DOI: 10.1139/g03-054] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) were developed for rye (Secale cereale L.). Suspensions of intact chromosomes were prepared by mechanical homogenization of synchronized root tips after mild fixation with formaldehyde. Histograms of relative fluorescence intensity obtained after the analysis of DAPI-stained chromosomes (flow karyotypes) were characterized and the chromosome content of the DNA peaks was determined. Chromosome 1R could be discriminated on a flow karyotype of S. cereale 'Imperial'. The remaining rye chromosomes (2R-7R) could be discriminated and sorted from individual wheat-rye addition lines. The analysis of lines with reconstructed karyotypes demonstrated a possibility of sorting translocation chromosomes. Supernumerary B chromosomes could be sorted from an experimental rye population and from S. cereale 'Adams'. Flow-sorted chromosomes were identified by fluorescence in situ hybridization (FISH) with probes for various DNA repeats. Large numbers of chromosomes of a single type sorted onto microscopic slides facilitated detection of rarely occurring chromosome variants by FISH with specific probes. PCR with chromosome-specific primers confirmed the identity of sorted fractions and indicated suitability of sorted chromosomes for physical mapping. The possibility to sort large numbers of chromosomes opens a way for the construction of large-insert chromosome-specific DNA libraries in rye.
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Affiliation(s)
- M Kubaláková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic
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50
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Hoshi Y, Nakayama T, Pląder W, Malepszy S, Doležel J. The Effects of DNA Synthesis Inhibitors on Cell Cycle Synchronization in Cucumber (Cucumis sativus L.) Root Meristems. CYTOLOGIA 2004. [DOI: 10.1508/cytologia.69.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoshikazu Hoshi
- Department of Chemical and Biological Engineering, Ariake National College of Technology, Japan
| | - Takayuki Nakayama
- Department of Chemical and Biological Engineering, Ariake National College of Technology, Japan
| | - Wojciech Pląder
- Department of Plant Genetics and Biotechnology, Warsaw Agricultural University
| | - Stefan Malepszy
- Department of Plant Genetics and Biotechnology, Warsaw Agricultural University
| | - Jaroslav Doležel
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic
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