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Ali M, Polgári D, Sepsi A, Kontra L, Dalmadi Á, Havelda Z, Sági L, Kis A. Correction: Rapid and cost-effective molecular karyotyping in wheat, barley, and their crossprogeny by chromosome-specific multiplex PCR. Plant Methods 2024; 20:55. [PMID: 38641614 PMCID: PMC11031907 DOI: 10.1186/s13007-024-01179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Mohammad Ali
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
- , Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
| | - Dávid Polgári
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
- , Centre for Agricultural Research, Hungarian Research Network,, 2462, Martonvásár, Hungary
- , Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, , 2462, Martonvásár, Hungary
| | - Adél Sepsi
- , Centre for Agricultural Research, Hungarian Research Network,, 2462, Martonvásár, Hungary
| | - Levente Kontra
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
- , Institute of Experimental Medicine, Bioinformatics Core Facility, Hungarian Research Network,, 1083, Budapest, Hungary
| | - Ágnes Dalmadi
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
- , Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
| | - Zoltán Havelda
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
- , Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
| | - László Sági
- , Centre for Agricultural Research, Hungarian Research Network,, 2462, Martonvásár, Hungary.
- , Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, , 2462, Martonvásár, Hungary.
| | - András Kis
- , Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences,, 2100, Gödöllő, Hungary
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Ali M, Polgári D, Sepsi A, Kontra L, Dalmadi Á, Havelda Z, Sági L, Kis A. Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR. Plant Methods 2024; 20:37. [PMID: 38444026 PMCID: PMC10913579 DOI: 10.1186/s13007-024-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Interspecific hybridisation is a powerful tool for increasing genetic diversity in plant breeding programmes. Hexaploid wheat (Triticum aestivum, 2n = 42) × barley (Hordeum vulgare, 2n = 14) intergeneric hybrids can contribute to the transfer of agronomically useful traits by creating chromosome addition or translocation lines as well as full hybrids. Information on the karyotype of hybrid progenies possessing various combinations of wheat and barley chromosomes is thus essential for the subsequent breeding steps. Since the standard technique of chromosome in situ hybridisation is labour-intensive and requires specific skills. a routine, cost-efficient, and technically less demanding approach is beneficial both for research and breeding. RESULTS We developed a Multiplex Polymerase Chain Reaction (MPCR) method to identify individual wheat and barley chromosomes. Chromosome-specific primer pairs were designed based on the whole genome sequences of 'Chinese Spring' wheat and 'Golden Promise' barley as reference cultivars. A pool of potential primers was generated by applying a 20-nucleotide sliding window with consecutive one-nucleotide shifts on the reference genomes. After filtering for optimal primer properties and defined amplicon sizes to produce an ordered ladder-like pattern, the primer pool was manually curated and sorted into four MPCR primer sets for the wheat A, B, and D sub-genomes, and for the barley genome. The designed MPCR primer sets showed high chromosome specificity in silico for the genome sequences of all 18 wheat and barley cultivars tested. The MPCR primers proved experimentally also chromosome-specific for the reference cultivars as well as for 13 additional wheat and four barley genotypes. Analyses of 16 wheat × barley F1 hybrid plants demonstrated that the MPCR primer sets enable the fast and one-step detection of all wheat and barley chromosomes. Finally, the established genotyping system was fully corroborated with the standard genomic in situ hybridisation (GISH) technique. CONCLUSIONS Wheat and barley chromosome-specific MPCR offers a fast, labour-friendly, and versatile alternative to molecular cytogenetic detection of individual chromosomes. This method is also suitable for the high-throughput analysis of distinct (sub)genomes, and, in contrast to GISH, can be performed with any tissue type. The designed primer sets proved to be highly chromosome-specific over a wide range of wheat and barley genotypes as well as in wheat × barley hybrids. The described primer design strategy can be extended to many species with precise genome sequence information.
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Affiliation(s)
- Mohammad Ali
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Dávid Polgári
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary
| | - Levente Kontra
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Institute of Experimental Medicine, Bioinformatics Core Facility, Hungarian Research Network, Budapest, 1083, Hungary
| | - Ágnes Dalmadi
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Zoltán Havelda
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - László Sági
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary.
| | - András Kis
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary.
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Mihók E, Polgári D, Lenykó-Thegze A, Makai D, Fábián A, Ali M, Kis A, Sepsi A, Sági L. Plasticity of parental CENH3 incorporation into the centromeres in wheat × barley F1 hybrids. Front Plant Sci 2024; 15:1324817. [PMID: 38313805 PMCID: PMC10834757 DOI: 10.3389/fpls.2024.1324817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024]
Abstract
Incorporating the centromere-specific histone H3 protein CENH3 into the centromeric nucleosomes is indispensable for accurate centromere function and balanced chromosome segregation in most eukaryotes, including higher plants. In the cell nuclei of interspecific hybrids, divergent centromeric DNAs cohabit and lead the corresponding parental chromosomes through the mitotic and meiotic cell divisions. Depending on the transmission of the parental chromosomes carrying the CENH3-encoding genes, CENH3 proteins from one or both parents may be present in these hybrids. The incorporation of parental CENH3 proteins into the divergent centromeres and their role in the chromosome elimination process in interspecific hybrids is still poorly understood. Here, we produced wheat × barley F1 hybrids that carried different combinations of barley chromosomes with genes encoding for either one (αCENH3) or both barley CENH3 protein variants (α- and βCENH3). We generated specific antibodies distinguishing between the wheat CENH3 proteins and barley αCENH3 and applied them together with FISH probes to detect the precise pattern of parental CENH3 deposition into the wheat and barley centromeric nucleosomes. Analysis of somatic and meiotic nuclei of the wheat × barley hybrids revealed the plasticity of the maternal (wheat) CENH3 proteins to become incorporated into the paternal (barley) centromeric nucleosomes. However, no evidence for paternal CENH3 plasticity was detected in this study. The significance of the unilateral centromere plasticity and possible patterns of CENH3 incorporation into centromeres in interspecific hybrids are discussed.
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Affiliation(s)
- Edit Mihók
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Dávid Polgári
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, Hungary
| | - Andrea Lenykó-Thegze
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - Diána Makai
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Attila Fábián
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - Mohammad Ali
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - András Kis
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - László Sági
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, Hungary
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Cseh A, Lenykó-Thegze A, Makai D, Szabados F, Hamow KÁ, Gulyás Z, Kiss T, Karsai I, Moncsek B, Mihók E, Sepsi A. Meiotic instability and irregular chromosome pairing underpin heat-induced infertility in bread wheat carrying the Rht-B1b or Rht-D1b Green Revolution genes. New Phytol 2024; 241:180-196. [PMID: 37691304 DOI: 10.1111/nph.19256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023]
Abstract
Mutations in the Rht-B1a and Rht-D1a genes of wheat (Triticum aestivum; resulting in Rht-B1b and Rht-D1b alleles) cause gibberellin-insensitive dwarfism and are one of the most important elements of increased yield introduced during the 'Green Revolution'. We measured the effects of a short period of heat imposed during the early reproductive stage on near-isogenic lines carrying Rht-B1b or Rht-D1b alleles, with respect to the wild-type (WT). The temperature shift caused a significant fertility loss within the ears of Rht-B1b and Rht-D1b wheats, greater than that observed for the WT. Defects in chromosome synapsis, reduced homologous recombination and a high frequency of chromosome mis-segregation were associated with reduced fertility. The transcription of TaGA3ox gene involved in the final stage of gibberellic acid (GA) biosynthesis was activated and ultra-performance liquid chromatography-tandem mass spectrometry identified GA1 as the dominant bioactive GA in developing ears, but levels were unaffected by the elevated temperature. Rht-B1b and Rht-D1b mutants were inclined to meiotic errors under optimal temperatures and showed a higher susceptibility to heat than their tall counterparts. Identification and introduction of new dwarfing alleles into modern breeding programmes is invaluable in the development of climate-resilient wheat varieties.
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Affiliation(s)
- András Cseh
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Andrea Lenykó-Thegze
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Diána Makai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Fanni Szabados
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Kamirán Áron Hamow
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Zsolt Gulyás
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Tibor Kiss
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eszterházy tér 1, Eger, 3300, Hungary
| | - Ildikó Karsai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Blanka Moncsek
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Edit Mihók
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Adél Sepsi
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
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Makai D, Mihók E, Polgári D, Cseh A, Lenykó-Thegze A, Sepsi A, Sági L. Rapid in-solution preparation of somatic and meiotic plant cell nuclei for high-quality 3D immunoFISH and immunoFISH-GISH. Plant Methods 2023; 19:80. [PMID: 37553677 PMCID: PMC10408160 DOI: 10.1186/s13007-023-01061-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/22/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND Though multicolour labelling methods allow the routine detection of a wide range of fluorescent (immuno)probe types in molecular cytogenetics, combined applications for the simultaneous in situ detection of proteins and nucleic acids are still sporadic in plant cell biology. A major bottleneck has been the availability of high-quality plant nuclei with a balance between preservation of 3D ultrastructure and maintaining immunoreactivity. The aim of this study was to develop a quick and reliable procedure to prepare plant nuclei suitable for various combinations of immunolabelling and fluorescence in situ hybridisation methods (immunoFISH-GISH). RESULTS The mechanical removal of the cell wall and cytoplasm, instead of enzymatic degradation, resulted in a gentle, yet effective, cell permeabilisation. Rather than manually releasing the nuclei from the fixed tissues, the procedure involves in-solution cell handling throughout the fixation and the preparation steps as ended with pipetting the pure nuclei suspension onto microscope slides. The optimisation of several critical steps is described in detail. Finally, the procedure is shown to be compatible with immunolabelling, FISH and GISH as well as their simultaneous combinations. CONCLUSION A simple plant cell nuclei preparation procedure was developed for combined immunolabelling-in situ hybridisation methods. The main and critical elements of the procedure are: a short period of fixation, incorporation of detergents to facilitate the fixation of tissues and the penetration of probes, tissue grinding to eliminate unwanted cell components, and an optimal buffer to handle nuclei. The procedure is time efficient and is easily transferable without prior expertise.
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Affiliation(s)
- Diána Makai
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Edit Mihók
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Dávid Polgári
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - András Cseh
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
| | - Andrea Lenykó-Thegze
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, 2462, Hungary.
| | - László Sági
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary.
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Makai D, Cseh A, Sepsi A, Makai S. A Multigraph-Based Representation of Hi-C Data. Genes (Basel) 2022; 13:genes13122189. [PMID: 36553456 PMCID: PMC9778156 DOI: 10.3390/genes13122189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Chromatin-chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to environmental stimuli, the linear sequence information needs to be interpreted in three-dimensional space, which is still a challenging task. Here, we propose a novel, heuristic approach to represent Hi-C datasets by a whole-genomic pseudo-structure in 3D space. The baseline of our approach is the construction of a multigraph from genomic-sequence data and Hi-C interaction data, then applying a modified force-directed layout algorithm. The resulting layout is a pseudo-structure. While pseudo-structures are not based on direct observation and their details are inherent to settings, surprisingly, they demonstrate interesting, overall similarities of known genome structures of both barley and rice, namely, the Rabl and Rosette-like conformation. It has an exciting potential to be extended by additional omics data (RNA-seq, Chip-seq, etc.), allowing to visualize the dynamics of the pseudo-structures across various tissues or developmental stages. Furthermore, this novel method would make it possible to revisit most Hi-C data accumulated in the public domain in the last decade.
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Affiliation(s)
- Diána Makai
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, 2462 Martonvásár, Hungary
| | - András Cseh
- Department of Molecular Breeding, Eötvös Loránd Research Network, Centre for Agricultural Research, 2462 Martonvásár, Hungary
| | - Adél Sepsi
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, 2462 Martonvásár, Hungary
| | - Szabolcs Makai
- Department of Molecular Breeding, Eötvös Loránd Research Network, Centre for Agricultural Research, 2462 Martonvásár, Hungary
- Department of Cereal Breeding, Eötvös Loránd Research Network, Centre for Agricultural Research, 2462 Martonvásár, Hungary
- Correspondence:
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Lenykó-Thegze A, Fábián A, Mihók E, Makai D, Cseh A, Sepsi A. Pericentromeric chromatin reorganisation follows the initiation of recombination and coincides with early events of synapsis in cereals. Plant J 2021; 107:1585-1602. [PMID: 34171148 DOI: 10.1111/tpj.15391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The reciprocal exchange of genetic information between homologous chromosomes during meiotic recombination is essential to secure balanced chromosome segregation and to promote genetic diversity. The chromosomal position and frequency of reciprocal genetic exchange shapes the efficiency of breeding programmes and influences crop improvement under a changing climate. In large genome cereals, such as wheat and barley, crossovers are consistently restricted to subtelomeric chromosomal regions, thus preventing favourable allele combinations being formed within a considerable proportion of the genome, including interstitial and pericentromeric chromatin. Understanding the key elements driving crossover designation is therefore essential to broaden the regions available for crossovers. Here, we followed early meiotic chromatin dynamism in cereals through the visualisation of a homologous barley chromosome arm pair stably transferred into the wheat genetic background. By capturing the dynamics of a single chromosome arm at the same time as detecting the undergoing events of meiotic recombination and synapsis, we showed that subtelomeric chromatin of homologues synchronously transitions to an open chromatin structure during recombination initiation. By contrast, pericentromeric and interstitial regions preserved their closed chromatin organisation and become unpackaged only later, concomitant with initiation of recombinatorial repair and the initial assembly of the synaptonemal complex. Our results raise the possibility that the closed pericentromeric chromatin structure in cereals may influence the fate decision during recombination initiation, as well as the spatial development of synapsis, and may also explain the suppression of crossover events in the proximity of the centromeres.
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Affiliation(s)
- Andrea Lenykó-Thegze
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Attila Fábián
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Edit Mihók
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Diána Makai
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - András Cseh
- Department of Molecular Breeding, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Adél Sepsi
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Department of Applied Biotechnology and Food Science (ABÉT), BME, Budapest University of Technology and Economics, Műegyetem rkp. 3-9, Budapest, 1111, Hungary
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Sepsi A, Schwarzacher T. Chromosome-nuclear envelope tethering - a process that orchestrates homologue pairing during plant meiosis? J Cell Sci 2020; 133:133/15/jcs243667. [PMID: 32788229 PMCID: PMC7438012 DOI: 10.1242/jcs.243667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome. Here, we review advances on chromosome behaviour during meiotic prophase I in higher plants, by integrating centromere- and telomere dynamics driven by cytoskeletal motor proteins, into the processes of homologue pairing, synapsis and recombination. Centromere–centromere associations and the gathering of telomeres at the onset of meiosis at opposite nuclear poles create a spatially organised and restricted nuclear state in which homologous DNA interactions are favoured but ectopic interactions also occur. The release and dispersion of centromeres from the nuclear periphery increases the motility of chromosome arms, allowing meiosis-specific movements that disrupt ectopic interactions. Subsequent expansion of interstitial synapsis from numerous homologous interactions further corrects ectopic interactions. Movement and organisation of chromosomes, thus, evolved to facilitate the pairing process, and can be modulated by distinct stages of chromatin associations at the nuclear envelope and their collective release. Summary: We review plant meiosis, including chromosome tethering at the nuclear periphery that, we propose, defines chromosome dynamics-facilitating DNA sequence-based pairing of homologues
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Affiliation(s)
- Adél Sepsi
- Department of Plant Cell Biology, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary .,BME Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science (ABÉT), 1111, Budapest, Mu˝ egyetem rkp. 3-9., Hungary
| | - Trude Schwarzacher
- University of Leicester, Department of Genetics and Genome Biology, University Road, Leicester LE1 7RH, UK.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Sepsi A, Fábián A, Jäger K, Heslop-Harrison JS, Schwarzacher T. ImmunoFISH: Simultaneous Visualisation of Proteins and DNA Sequences Gives Insight Into Meiotic Processes in Nuclei of Grasses. Front Plant Sci 2018; 9:1193. [PMID: 30154816 PMCID: PMC6102387 DOI: 10.3389/fpls.2018.01193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 05/04/2023]
Abstract
ImmunoFISH is a method combining immunolabelling (IL) with fluorescent in situ hybridisation (FISH) to simultaneously detect the nuclear distribution of proteins and specific DNA sequences within chromosomes. This approach is particularly important when analysing meiotic cell division where morphogenesis of individual proteins follows stage-specific changes and is accompanied by a noticeable chromatin dynamism. The method presented here is simple and provides reliable results of high quality signal, low background staining and can be completed within 2 days following preparation. Conventional widefield epifluorescent or laser scanning microscopy can be used for high resolution and three-dimensional analysis. Fixation and preparation techniques were optimised to best preserve nuclear morphology and protein epitopes without the need for any antigen retrieval. Preparation of plant material involved short cross-linking fixation of meiotic tissues with paraformaldehyde (PFA) followed by enzyme digestion and slide-mounting. In order to avoid rapid sample degradation typical of shortly fixed plant materials, and to be able to perform IL later, slides were snap-frozen and stored at -80°C. Ultra-freezing produced a remarkable degree of structural preservation for up to 12 months, whereby sample quality was similar to that of fresh material. Harsh chemicals and sample dehydration were avoided throughout the procedure and permeability was ensured by a 0.1-0.3% detergent treatment. The ImmunoFISH method was developed specifically for studying meiosis in Triticeae, but should also be applicable to other grass and plant species.
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Affiliation(s)
- Adél Sepsi
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- *Correspondence: Adél Sepsi ;,
| | - Attila Fábián
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Katalin Jäger
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - J. S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Sepsi A, Higgins JD, Heslop-Harrison JSP, Schwarzacher T. CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat. Plant J 2017; 89:235-249. [PMID: 27624968 DOI: 10.1111/tpj.13379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/04/2016] [Accepted: 09/08/2016] [Indexed: 05/02/2023]
Abstract
During meiosis, centromeres in some species undergo a series of associations, but the processes and progression to homologous pairing is still a matter of debate. Here, we aimed to correlate meiotic centromere dynamics and early telomere behaviour to the progression of synaptonemal complex (SC) construction in hexaploid wheat (2n = 42) by triple immunolabelling of CENH3 protein marking functional centromeres, and SC proteins ASY1 (unpaired lateral elements) and ZYP1 (central elements in synapsed chromosomes). We show that single or multiple centromere associations formed in meiotic interphase undergo a progressive polarization (clustering) at the nuclear periphery in early leptotene, leading to formation of the telomere bouquet. Critically, immunolabelling shows the dynamics of these presynaptic centromere associations and a structural reorganization of the centromeric chromatin coinciding with key events of synapsis initiation from the subtelomeric regions. As short stretches of subtelomeric synapsis emerged at early zygotene, centromere clusters lost their strong polarization, gradually resolving as individual centromeres indicated by more than 21 CENH3 foci associated with unpaired lateral elements. Only following this centromere depolarization were homologous chromosome arms connected, as observed by the alignment and fusion of interstitial ZYP1 loci elongating at zygotene so synapsis at centromeres is a continuation of the interstitial synapsis. Our results thus reveal that centromere associations are a component of the timing and progression of chromosome synapsis, and the gradual release of the individual centromeres from the clusters correlates with the elongation of interstitial synapsis between the corresponding homologues.
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Affiliation(s)
- Adél Sepsi
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - James D Higgins
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
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Kruppa K, Sepsi A, Szakács É, Röder MS, Molnár-Láng M. Characterization of a 5HS-7DS.7DL wheat-barley translocation line and physical mapping of the 7D chromosome using SSR markers. J Appl Genet 2013; 54:251-8. [DOI: 10.1007/s13353-013-0152-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 11/25/2022]
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12
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Linc G, Sepsi A, Molnár-Láng M. A FISH Karyotype to Study Chromosome Polymorphisms for the Elytrigia elongata E Genome. Cytogenet Genome Res 2012; 136:138-44. [DOI: 10.1159/000334835] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2011] [Indexed: 11/19/2022] Open
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13
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Georgieva M, Sepsi A, Tyankova N, Molnár-Láng M. Molecular cytogenetic characterization of two high protein wheat-Thinopyrum intermedium partial amphiploids. J Appl Genet 2011; 52:269-77. [PMID: 21404041 DOI: 10.1007/s13353-011-0037-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 02/26/2011] [Indexed: 11/26/2022]
Abstract
Fluorescence and genomic in situ hybridization (FISH and GISH) were used to establish the cytogenetic constitution of two wheat × Thinopyrum intermedium partial amphiploids H95 and 55(1-57). Both partial amphiploids are high-protein lines having resistance to leaf rust, yellow rust and powdery mildew and have in total 56 chromosomes per cell. Repetitive DNA probes (pTa71, Afa family and pSc119.2) were used to identify the individual wheat chromosomes and to reveal the distribution of these probes within the alien chromosomes. FISH detected 6B tetrasomy in H95 and a null (1D)-tetrasomy (1B) in 55(1-57). GISH was carried out using biotin labeled Th. intermedium DNA and digoxigenin labeled Pseudoroegneria spicata DNA as probes, subsequently. GISH results revealed 44 wheat chromosomes and four Thinopyrum chromosome pairs, including three S and one J chromosome pairs in line H95. Line 55(1-57), contained 42 wheat chromosomes and six Th. intermedium pairs, including two S and one J(S) pairs. Additionally, two identical translocated chromosome pairs with diminished affinity to the alien chromatin were detected in both amphiploids. Another two translocations were found in 55(1-57), with satellite sections from the Thinopyrum J genome.
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Affiliation(s)
- Mariyana Georgieva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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14
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Sepsi A, Molnár I, Molnár-Láng M. Physical mapping of a 7A.7D translocation in the wheat-Thinopyrum ponticum partial amphiploid BE-1 using multicolour genomic in situ hybridization and microsatellite marker analysis. Genome 2010; 52:748-54. [PMID: 19935922 DOI: 10.1139/g09-047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The absence of chromosome 7D in the wheat-Thinopyrum ponticum partial amphiploid BE-1 was detected previously by multicolour genomic in situ hybridization, sequential FISH (fluorescence in situ hybridization) using repetitive DNA probes, and SSR marker analysis. In the present study the previous cytogenetic and SSR marker analyses were expanded to include 25 other SSR markers assigned to wheat chromosomes 7A and 7D to confirm the presence of a 7A.7D translocation and to specify its composition. An almost complete chromosome 7A and a short chromosome segment derived from the terminal region of 7DL were detected, confirming the presence of a terminal translocation involving the distal regions of 7AL and 7DL. In both cases the position of the translocation breakpoint was different from that of known deletion lines. The identification of the 7AL.7DL translocation and its breakpoint position provides a new physical landmark for future physical mapping studies, opening up the possibility of more precise localization of genes or molecular markers within the terminal regions of 7DL and 7AL.
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Affiliation(s)
- A Sepsi
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvasar, P.O. Box 19, Hungary
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15
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Sepsi A, Molnár I, Szalay D, Molnár-Láng M. Characterization of a leaf rust-resistant wheat-Thinopyrum ponticum partial amphiploid BE-1, using sequential multicolor GISH and FISH. Theor Appl Genet 2008; 116:825-34. [PMID: 18224300 DOI: 10.1007/s00122-008-0716-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 01/08/2008] [Indexed: 05/19/2023]
Abstract
In situ hybridization (multicolor GISH and FISH) was used to characterize the genomic composition of the wheat-Thinopyrum ponticum partial amphiploid BE-1. The amphiploid is a high-protein line having resistance to leaf rust (Puccinia recondita f. sp. tritici) and powdery mildew (Blumeria graminis f. sp. tritici) and has in total 56 chromosomes per cell. Multicolor GISH using J, A and D genomic probes showed 16 chromosomes originating from Thinopyrum ponticum and 14 A genome, 14 B genome and 12 D genome chromosomes. Six of the Th. ponticum chromosomes carried segments different from the J genome in their centromeric regions. It was demonstrated that these alien chromosome segments did not originate from the A, B or D genomes of wheat, so the translocation chromosomes were considered to be J(s) type chromosomes carrying segments similar to the S genome near the centromeres. Rearrangements between the A and D genomes of wheat were detected. FISH using Afa family, pSc119.2 and pTa71 probes allowed the identification of all the wheat chromosomes present and the determination of the chromosomes involved in the translocations. The 4A and 7A chromosomes were identified as being involved in intergenomic translocations. The replaced wheat chromosome was identified as 7D. The localization of these repetitive DNA clones on the Th. ponticum chromosomes of the amphiploid was described in the present study. On the basis of their multicolor FISH patterns, the alien chromosomes could be arranged in eight pairs and could also be differentiated unequivocally from each other.
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Affiliation(s)
- A Sepsi
- Agricultural Research Institute of the Hungarian Academy of Sciences, 2462, Martonvásár, Hungary
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16
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Fekete E, Karaffa L, Sándor E, Bányai I, Seiboth B, Gyémánt G, Sepsi A, Szentirmai A, Kubicek CP. The alternative D-galactose degrading pathway of Aspergillus nidulans proceeds via L-sorbose. Arch Microbiol 2003; 181:35-44. [PMID: 14624333 DOI: 10.1007/s00203-003-0622-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Revised: 10/14/2003] [Accepted: 10/17/2003] [Indexed: 11/29/2022]
Abstract
The catabolism of d-galactose in yeast depends on the enzymes of the Leloir pathway. In contrast, Aspergillus nidulans mutants in galactokinase ( galE) can still grow on d-galactose in the presence of ammonium-but not nitrate-ions as nitrogen source. A. nidulans galE mutants transiently accumulate high (400 mM) intracellular concentrations of galactitol, indicating that the alternative d-galactose degrading pathway may proceed via this intermediate. The enzyme degrading galactitol was identified as l-arabitol dehydrogenase, because an A. nidulans loss-of-function mutant in this enzyme ( araA1) did not show NAD(+)-dependent galactitol dehydrogenase activity, still accumulated galactitol but was unable to catabolize it thereafter, and a double galE/araA1 mutant was unable to grow on d-galactose or galactitol. The product of galactitol oxidation was identified as l-sorbose, which is a substrate for hexokinase, as evidenced by a loss of l-sorbose phosphorylating activity in an A. nidulans hexokinase ( frA1) mutant. l-Sorbose catabolism involves a hexokinase step, indicated by the inability of the frA1 mutant to grow on galactitol or l-sorbose, and by the fact that a galE/frA1 double mutant of A. nidulans was unable to grow on d-galactose. The results therefore provide evidence for an alternative pathway of d-galactose catabolism in A. nidulans that involves reduction of the d-galactose to galactitol and NAD(+)-dependent oxidation of galactitol by l-arabitol dehydrogenase to l-sorbose.
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Affiliation(s)
- Erzsébet Fekete
- Department of Microbiology and Biotechnology, University of Debrecen, Faculty of Sciences, P.O.Box 63, 4010 Debrecen, Hungary
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17
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Karaffa L, Fekete E, Sándor E, Sepsi A, Seiboth B, Szentirmai A, Kubicek CP. Carbon catabolite repression in the regulation of beta-galactosidase activity in Aspergillus nidulans. Acta Microbiol Immunol Hung 2003; 49:261-5. [PMID: 12109156 DOI: 10.1556/amicr.49.2002.2-3.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- L Karaffa
- Department of Microbiology and Biotechnology, Faculty of Sciences, University of Debrecen, H-4010, P.O. Box 63, Debrecen, Hungary
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