1
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Morgan C, Howard M, Henderson IR. HEI10 coarsening, chromatin and sequence polymorphism shape the plant meiotic recombination landscape. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102570. [PMID: 38838583 DOI: 10.1016/j.pbi.2024.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Meiosis is a conserved eukaryotic cell division that produces spores required for sexual reproduction. During meiosis, chromosomes pair and undergo programmed DNA double-strand breaks, followed by homologous repair that can result in reciprocal crossovers. Crossover formation is highly regulated with typically few events per homolog pair. Crossovers additionally show wider spacing than expected from uniformly random placement - defining the phenomenon of interference. In plants, the conserved HEI10 E3 ligase is initially loaded along meiotic chromosomes, before maturing into a small number of foci, corresponding to crossover locations. We review the coarsening model that explains these dynamics as a diffusion and aggregation process, resulting in approximately evenly spaced HEI10 foci. We review how underlying chromatin states, and the presence of interhomolog polymorphisms, shape the meiotic recombination landscape, in light of the coarsening model. Finally, we consider future directions to understand the control of meiotic recombination in plant genomes.
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Affiliation(s)
- Chris Morgan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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2
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Osman K, Desjardins SD, Simmonds J, Burridge AJ, Kanyuka K, Henderson IR, Edwards KJ, Uauy C, Franklin FCH, Higgins JD, Sanchez-Moran E. FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis. THE NEW PHYTOLOGIST 2024. [PMID: 38584326 DOI: 10.1111/nph.19716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1-3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position. We analysed figl1 mutants and virus-induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid. FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1-fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals. Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding.
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Affiliation(s)
- Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
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3
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Zhang Z, Guo YY, Wang YC, Zhou L, Fan J, Mao YC, Yang YM, Zhang YF, Huang XH, Zhu J, Zhang C, Yang ZN. A point mutation in the meiotic crossover formation gene HEI10/TFS2 leads to thermosensitive genic sterility in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:506-518. [PMID: 38169508 DOI: 10.1111/tpj.16621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Thermosensitive genic female sterility (TGFS) is a promising property to be utilized for hybrid breeding. Here, we identified a rice TGFS line, tfs2, through an ethyl methyl sulfone (EMS) mutagenesis strategy. This line showed sterility under high temperature and became fertile under low temperature. Few seeds were produced when the tfs2 stigma was pollinated, indicating that tfs2 is female sterile. Gene cloning and genetic complementation showed that a point mutation from leucine to phenylalanine in HEI10 (HEI10tfs2), a crossover formation protein, caused the TGFS trait of tfs2. Under high temperature, abnormal univalents were formed, and the chromosomes were unequally segregated during meiosis, similar to the reported meiotic defects in oshei10. Under low temperature, the number of univalents was largely reduced, and the chromosomes segregated equally, suggesting that crossover formation was restored in tfs2. Yeast two-hybrid assays showed that HEI10 interacted with two putative protein degradation-related proteins, RPT4 and SRFP1. Through transient expression in tobacco leaves, HEI10 were found to spontaneously aggregate into dot-like foci in the nucleus under high temperature, but HEI10tfs2 failed to aggregate. In contrast, low temperature promoted HEI10tfs2 aggregation. This result suggests that protein aggregation at the crossover position contributes to the fertility restoration of tfs2 under low temperature. In addition, RPT4 and SRFP1 also aggregated into dot-like foci, and these aggregations depend on the presence of HEI10. These findings reveal a novel mechanism of fertility restoration and facilitate further understanding of HEI10 in meiotic crossover formation.
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Affiliation(s)
- Zheng Zhang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yu-Yi Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yi-Chen Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lei Zhou
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jing Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yi-Chen Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yan-Ming Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yan-Fei Zhang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xue-Hui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Cheng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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4
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Kim H, Kim J, Son N, Kuo P, Morgan C, Chambon A, Byun D, Park J, Lee Y, Park YM, Fozard JA, Guérin J, Hurel A, Lambing C, Howard M, Hwang I, Mercier R, Grelon M, Henderson IR, Choi K. Control of meiotic crossover interference by a proteolytic chaperone network. NATURE PLANTS 2024; 10:453-468. [PMID: 38379086 DOI: 10.1038/s41477-024-01633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Meiosis is a specialized eukaryotic division that produces genetically diverse gametes for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal exchanges, called crossovers, which recombine genetic variation. Meiotic crossovers are stringently controlled with at least one obligate exchange forming per chromosome pair, while closely spaced crossovers are inhibited by interference. In Arabidopsis, crossover positions can be explained by a diffusion-mediated coarsening model, in which large, approximately evenly spaced foci of the pro-crossover E3 ligase HEI10 grow at the expense of smaller, closely spaced clusters. However, the mechanisms that control HEI10 dynamics during meiosis remain unclear. Here, through a forward genetic screen in Arabidopsis, we identified high crossover rate3 (hcr3), a dominant-negative mutant that reduces crossover interference and increases crossovers genome-wide. HCR3 encodes J3, a co-chaperone related to HSP40, which acts to target protein aggregates and biomolecular condensates to the disassembly chaperone HSP70, thereby promoting proteasomal degradation. Consistently, we show that a network of HCR3 and HSP70 chaperones facilitates proteolysis of HEI10, thereby regulating interference and the recombination landscape. These results reveal a new role for the HSP40/J3-HSP70 chaperones in regulating chromosome-wide dynamics of recombination via control of HEI10 proteolysis.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Namil Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Chris Morgan
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Aurélie Chambon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngkyung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - John A Fozard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julie Guérin
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Aurélie Hurel
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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Li Y, Zhou Y, Wang B, Mu N, Miao Y, Tang D, Shen Y, Cheng Z. FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:717-727. [PMID: 37632767 DOI: 10.1111/tpj.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/11/2023] [Indexed: 08/28/2023]
Abstract
Crossovers (COs) are necessary for generating genetic diversity that breeders can select, but there are conserved mechanisms that regulate their frequency and distribution. Increasing CO frequency may raise the efficiency of selection by increasing the chance of integrating more desirable traits. In this study, we characterize rice FANCM and explore its functions in meiotic CO control. FANCM mutations do not affect fertility in rice, but they cause a great boost in the overall frequency of COs in both inbred and hybrid rice, according to genetic analysis of the complete set of fancm zmm (hei10, ptd, shoc1, mer3, zip4, msh4, msh5, and heip1) mutants. Although the early homologous recombination events proceed normally in fancm, the meiotic extra COs are not marked with HEI10 and require MUS81 resolvase for resolution. FANCM depends on PAIR1, COM1, DMC1, and HUS1 to perform its functions. Simultaneous disruption of FANCM and MEICA1 synergistically increases CO frequency, but it is accompanied by nonhomologous chromosome associations and fragmentations. FANCM interacts with the MHF complex, and ablation of rice MHF1 or MHF2 could restore the formation of 12 bivalents in the absence of the ZMM gene ZIP4. Our data indicate that unleashing meiotic COs by mutating any member of the FANCM-MHF complex could be an effective procedure to accelerate the efficiency of rice breeding.
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Affiliation(s)
- Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yue Zhou
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxin Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Mu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongjie Miao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
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6
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Rafiei N, Ronceret A. Crossover interference mechanism: New lessons from plants. Front Cell Dev Biol 2023; 11:1156766. [PMID: 37274744 PMCID: PMC10236007 DOI: 10.3389/fcell.2023.1156766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.
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Mehdi SMM, Szczesniak MW, Ludwików A. The Bro1-like domain-containing protein, AtBro1, modulates growth and abiotic stress responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1157435. [PMID: 37251780 PMCID: PMC10213323 DOI: 10.3389/fpls.2023.1157435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023]
Abstract
Abscisic acid (ABA) affects plant physiology by altering gene expression, enabling plants to adapt to a wide range of environments. Plants have evolved protective mechanisms to allow seed germination in harsh conditions. Here, we explore a subset of these mechanisms involving the AtBro1 gene, which encodes one of a small family of poorly characterised Bro1-like domain-containing proteins, in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts were upregulated by salt, ABA and mannitol stress, while AtBro1-overexpression lines demonstrated robust tolerance to drought and salt stress. Furthermore, we found that ABA elicits stress-resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 regulates drought resistance in Arabidopsis. When the AtBro1 promoter was fused to the β-glucuronidase (GUS) gene and introduced into plants, GUS was expressed mainly in rosette leaves and floral clusters, especially in anthers. Using a construct expressing an AtBro1-GFP fusion protein, AtBro1 was found to be localized in the plasma membrane in Arabidopsis protoplasts. A broad RNA-sequencing analysis revealed specific quantitative differences in the early transcriptional responses to ABA treatment between wild-type and loss-of-function bro1-1 mutant plants, suggesting that ABA stimulates stress-resistance responses via AtBro1. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in bro1-1 plants exposed to different stress conditions. Collectively, our results show that AtBro1 plays a significant role in the regulation of the plant transcriptional response to ABA and the induction of resistance responses to abiotic stress.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Agnieszka Ludwików
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
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Ziolkowski PA. Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism. PLANT REPRODUCTION 2023; 36:43-54. [PMID: 35819509 PMCID: PMC9958190 DOI: 10.1007/s00497-022-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 06/06/2023]
Abstract
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.
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Affiliation(s)
- Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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9
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Szymanska-Lejman M, Dziegielewski W, Dluzewska J, Kbiri N, Bieluszewska A, Poethig RS, Ziolkowski PA. The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids. Nat Commun 2023; 14:33. [PMID: 36596804 PMCID: PMC9810609 DOI: 10.1038/s41467-022-35722-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.
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Affiliation(s)
- Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Bieluszewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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10
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Jin C, Dong L, Wei C, Wani MA, Yang C, Li S, Li F. Creating novel ornamentals via new strategies in the era of genome editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1142866. [PMID: 37123857 PMCID: PMC10140431 DOI: 10.3389/fpls.2023.1142866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Ornamental breeding has traditionally focused on improving novelty, yield, quality, and resistance to biotic or abiotic stress. However, achieving these goals has often required laborious crossbreeding, while precise breeding techniques have been underutilized. Fortunately, recent advancements in plant genome sequencing and editing technology have opened up exciting new frontiers for revolutionizing ornamental breeding. In this review, we provide an overview of the current state of ornamental transgenic breeding and propose four promising breeding strategies that have already proven successful in crop breeding and could be adapted for ornamental breeding with the help of genome editing. These strategies include recombination manipulation, haploid inducer creation, clonal seed production, and reverse breeding. We also discuss in detail the research progress, application status, and feasibility of each of these tactics.
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Affiliation(s)
- Chunlian Jin
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Liqing Dong
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Chang Wei
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Muneeb Ahmad Wani
- Department of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Chunmei Yang
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
| | - Shenchong Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
| | - Fan Li
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, China
- *Correspondence: Fan Li, ; Shenchong Li,
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11
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Poethig RS, Cullina WL, Doody E, Floyd T, Fouracre JP, Hu T, Xu M, Zhao J. Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2022; 12:6677228. [PMID: 36018241 PMCID: PMC9526051 DOI: 10.1093/g3journal/jkac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/17/2022] [Indexed: 12/30/2022]
Abstract
Traffic lines are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 traffic lines that cover the Arabidopsis genome in overlapping intervals of approximately 1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here, we show how these lines enable a phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely linked mutations.
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Affiliation(s)
- R Scott Poethig
- Corresponding author: Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA.
| | - William L Cullina
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Erin Doody
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Taré Floyd
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | | | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA,Department of Biological Sciences, University of South Carolina, Charlottesville, SC 29208, USA
| | - Jianfei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
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12
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Differentiated function and localisation of SPO11-1 and PRD3 on the chromosome axis during meiotic DSB formation in Arabidopsis thaliana. PLoS Genet 2022; 18:e1010298. [PMID: 35857772 PMCID: PMC9342770 DOI: 10.1371/journal.pgen.1010298] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/01/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022] Open
Abstract
During meiosis, DNA double-strand breaks (DSBs) occur throughout the genome, a subset of which are repaired to form reciprocal crossovers between chromosomes. Crossovers are essential to ensure balanced chromosome segregation and to create new combinations of genetic variation. Meiotic DSBs are formed by a topoisomerase-VI-like complex, containing catalytic (e.g. SPO11) proteins and auxiliary (e.g. PRD3) proteins. Meiotic DSBs are formed in chromatin loops tethered to a linear chromosome axis, but the interrelationship between DSB-promoting factors and the axis is not fully understood. Here, we study the localisation of SPO11-1 and PRD3 during meiosis, and investigate their respective functions in relation to the chromosome axis. Using immunocytogenetics, we observed that the localisation of SPO11-1 overlaps relatively weakly with the chromosome axis and RAD51, a marker of meiotic DSBs, and that SPO11-1 recruitment to chromatin is genetically independent of the axis. In contrast, PRD3 localisation correlates more strongly with RAD51 and the chromosome axis. This indicates that PRD3 likely forms a functional link between SPO11-1 and the chromosome axis to promote meiotic DSB formation. We also uncovered a new function of SPO11-1 in the nucleation of the synaptonemal complex protein ZYP1. We demonstrate that chromosome co-alignment associated with ZYP1 deposition can occur in the absence of DSBs, and is dependent on SPO11-1, but not PRD3. Lastly, we show that the progression of meiosis is influenced by the presence of aberrant chromosomal connections, but not by the absence of DSBs or synapsis. Altogether, our study provides mechanistic insights into the control of meiotic DSB formation and reveals diverse functional interactions between SPO11-1, PRD3 and the chromosome axis. Most eukaryotes rely on the formation of gametes with half the number of chromosomes for sexual reproduction. Meiosis is a specialised type of cell division essential for the transition between a diploid and a haploid stage during gametogenesis. In early meiosis, programmed-DNA double strand breaks (DSBs) occur across the genome. These DSBs are processed by a set of proteins and the broken ends are repaired using the genetic information from the homologous chromosomes. These reciprocal exchanges of information between two chromosomes are called crossovers. Crossovers physical link chromosomes in pairs which is essential to ensure their correct segregation during the two rounds of meiotic division. Crossovers are also essential for the creation of genetic diversity as they break genetic linkages to form novel allelic blocks. The formation of DSBs is not completely understood in plants. Here we studied the function of SPO11-1 and PRD3, two proteins involved in the formation of DSBs in Arabidopsis. We discovered functional differences in their respective mode of recruitment to the chromosomes, their interactions with proteins forming the chromosome core and their roles in chromosome co-alignment. These indicate that, although SPO11-1 and PRD3 share a role in the formation of DSBs, the two proteins have additional and distinct roles beside DSB formation.
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13
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Kim J, Park J, Kim H, Son N, Kim E, Kim J, Byun D, Lee Y, Park YM, Nageswaran DC, Kuo P, Rose T, Dang TVT, Hwang I, Lambing C, Henderson IR, Choi K. Arabidopsis HEAT SHOCK FACTOR BINDING PROTEIN is required to limit meiotic crossovers and HEI10 transcription. EMBO J 2022; 41:e109958. [PMID: 35670129 PMCID: PMC9289711 DOI: 10.15252/embj.2021109958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
The number of meiotic crossovers is tightly controlled and most depend on pro-crossover ZMM proteins, such as the E3 ligase HEI10. Despite the importance of HEI10 dosage for crossover formation, how HEI10 transcription is controlled remains unexplored. In a forward genetic screen using a fluorescent crossover reporter in Arabidopsis thaliana, we identify heat shock factor binding protein (HSBP) as a repressor of HEI10 transcription and crossover numbers. Using genome-wide crossover mapping and cytogenetics, we show that hsbp mutations or meiotic HSBP knockdowns increase ZMM-dependent crossovers toward the telomeres, mirroring the effects of HEI10 overexpression. Through RNA sequencing, DNA methylome, and chromatin immunoprecipitation analysis, we reveal that HSBP is required to repress HEI10 transcription by binding with heat shock factors (HSFs) at the HEI10 promoter and maintaining DNA methylation over the HEI10 5' untranslated region. Our findings provide insights into how the temperature response regulator HSBP restricts meiotic HEI10 transcription and crossover number by attenuating HSF activity.
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Affiliation(s)
- Juhyun Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jihye Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Heejin Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Namil Son
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Eun‐Jung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jaeil Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Dohwan Byun
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Youngkyung Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Yeong Mi Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | | | - Pallas Kuo
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Teresa Rose
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Tuong Vi T Dang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Ildoo Hwang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Christophe Lambing
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Ian R Henderson
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Kyuha Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
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14
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Guo H, Stamper EL, Sato-Carlton A, Shimazoe MA, Li X, Zhang L, Stevens L, Tam KCJ, Dernburg AF, Carlton PM. Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity. eLife 2022; 11:77956. [PMID: 35758641 PMCID: PMC9278955 DOI: 10.7554/elife.77956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/23/2022] [Indexed: 12/28/2022] Open
Abstract
In the first meiotic cell division, proper segregation of chromosomes in most organisms depends on chiasmata, exchanges of continuity between homologous chromosomes that originate from the repair of programmed double-strand breaks (DSBs) catalyzed by the Spo11 endonuclease. Since DSBs can lead to irreparable damage in germ cells, while chromosomes lacking DSBs also lack chiasmata, the number of DSBs must be carefully regulated to be neither too high nor too low. Here, we show that in Caenorhabditis elegans, meiotic DSB levels are controlled by the phosphoregulation of DSB-1, a homolog of the yeast Spo11 cofactor Rec114, by the opposing activities of PP4PPH-4.1 phosphatase and ATRATL-1 kinase. Increased DSB-1 phosphorylation in pph-4.1 mutants correlates with reduction in DSB formation, while prevention of DSB-1 phosphorylation drastically increases the number of meiotic DSBs both in pph-4.1 mutants and in the wild-type background. C. elegans and its close relatives also possess a diverged paralog of DSB-1, called DSB-2, and loss of dsb-2 is known to reduce DSB formation in oocytes with increasing age. We show that the proportion of the phosphorylated, and thus inactivated, form of DSB-1 increases with age and upon loss of DSB-2, while non-phosphorylatable DSB-1 rescues the age-dependent decrease in DSBs in dsb-2 mutants. These results suggest that DSB-2 evolved in part to compensate for the inactivation of DSB-1 through phosphorylation, to maintain levels of DSBs in older animals. Our work shows that PP4PPH-4.1, ATRATL-1, and DSB-2 act in concert with DSB-1 to promote optimal DSB levels throughout the reproductive lifespan.
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Affiliation(s)
- Heyun Guo
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Ericca L Stamper
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aya Sato-Carlton
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Masa A Shimazoe
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan.,Department of Science, Kyoto University, Kyoto, Japan
| | - Xuan Li
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Liangyu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - K C Jacky Tam
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Abby F Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Peter M Carlton
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan.,Radiation Biology Center, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
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15
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Desjardins SD, Simmonds J, Guterman I, Kanyuka K, Burridge AJ, Tock AJ, Sanchez-Moran E, Franklin FCH, Henderson IR, Edwards KJ, Uauy C, Higgins JD. FANCM promotes class I interfering crossovers and suppresses class II non-interfering crossovers in wheat meiosis. Nat Commun 2022; 13:3644. [PMID: 35752733 PMCID: PMC9233680 DOI: 10.1038/s41467-022-31438-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
FANCM suppresses crossovers in plants by unwinding recombination intermediates. In wheat, crossovers are skewed toward the chromosome ends, thus limiting generation of novel allelic combinations. Here, we observe that FANCM maintains the obligate crossover in tetraploid and hexaploid wheat, thus ensuring that every chromosome pair exhibits at least one crossover, by localizing class I crossover protein HEI10 at pachytene. FANCM also suppresses class II crossovers that increased 2.6-fold in fancm msh5 quadruple mutants. These data are consistent with a role for FANCM in second-end capture of class I designated crossover sites, whilst FANCM is also required to promote formation of non-crossovers. In hexaploid wheat, genetic mapping reveals that crossovers increase by 31% in fancm compared to wild type, indicating that fancm could be an effective tool to accelerate breeding. Crossover rate differences in fancm correlate with wild type crossover distributions, suggesting that chromatin may influence the recombination landscape in similar ways in both wild type and fancm. The FANCM helicase functions in limiting crossovers (COs) by unwinding inter-homolog repair intermediates. Here, the authors generate null mutants of fancm in tetraploid and hexaploid wheat and show that FANCM promotes class I interfering COs and suppresses class II noninterfering COs in wheat meiosis.
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Affiliation(s)
- Stuart D Desjardins
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Inna Guterman
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Kostya Kanyuka
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.,Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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16
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Kim H, Choi K. Fast and Precise: How to Measure Meiotic Crossovers in Arabidopsis. Mol Cells 2022; 45:273-283. [PMID: 35444069 PMCID: PMC9095510 DOI: 10.14348/molcells.2022.2054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022] Open
Abstract
During meiosis, homologous chromosomes (homologs) pair and undergo genetic recombination via assembly and disassembly of the synaptonemal complex. Meiotic recombination is initiated by excess formation of DNA double-strand breaks (DSBs), among which a subset are repaired by reciprocal genetic exchange, called crossovers (COs). COs generate genetic variations across generations, profoundly affecting genetic diversity and breeding. At least one CO between homologs is essential for the first meiotic chromosome segregation, but generally only one and fewer than three inter-homolog COs occur in plants. CO frequency and distribution are biased along chromosomes, suppressed in centromeres, and controlled by pro-CO, anti-CO, and epigenetic factors. Accurate and high-throughput detection of COs is important for our understanding of CO formation and chromosome behavior. Here, we review advanced approaches that enable precise measurement of the location, frequency, and genomic landscapes of COs in plants, with a focus on Arabidopsis thaliana.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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17
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Kbiri N, Dluzewska J, Henderson IR, Ziolkowski PA. Quantifying Meiotic Crossover Recombination in Arabidopsis Lines Expressing Fluorescent Reporters in Seeds Using SeedScoring Pipeline for CellProfiler. Methods Mol Biol 2022; 2484:121-134. [PMID: 35461449 DOI: 10.1007/978-1-0716-2253-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The number of crossovers during meiosis is relatively low, so multiple meioses need to be analyzed to accurately measure crossover frequency. In Arabidopsis, systems based on the segregation of fluorescent T-DNA reporters that are expressed in seeds (fluorescent-tagged lines, FTLs) allow for an accurate measurement of crossover frequency in specific chromosome regions. A major advantage of FTL-based experiments is the ability to analyze thousands of seeds for each biological replicate, which requires the use of automatic seed scoring. Here, we describe a protocol to computationally count the proportion of seeds that experienced a crossover event within the tested FTL interval and so measure the recombination frequency within that interval. We describe SeedScoring, a CellProfiler pipeline where the total time needed to measure crossover frequency in a single FTL line is approximately 5 min using a series of three images taken under a fluorescent stereomicroscope (3 min) and passing these images through the SeedScoring pipeline described in this protocol (2 min).
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Affiliation(s)
- Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
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18
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Bieluszewski T, Szymanska-Lejman M, Dziegielewski W, Zhu L, Ziolkowski PA. Efficient Generation of CRISPR/Cas9-Based Mutants Supported by Fluorescent Seed Selection in Different Arabidopsis Accessions. Methods Mol Biol 2022; 2484:161-182. [PMID: 35461452 DOI: 10.1007/978-1-0716-2253-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Investigating the process of gamete formation in plants often requires the use of mutants of selected genes in various genetic backgrounds. For example, analysis of meiotic recombination based on sequencing or genotyping requires the generation of hybrids between two lines. Although T-DNA mutant collections of Arabidopsis thaliana are vast and easily accessible, they are largely confined to Col-0 background. This chapter describes how to efficiently generate knock-out mutants in different Arabidopsis accessions using CRISPR/Cas9 technology. The presented system is based on designing two single-guide RNAs (sgRNAs), which direct the Cas9 endonuclease to generate double-strand breaks at two sites, leading to genomic deletion in targeted gene. The presence of seed-expressed dsRed fluorescence cassette in the CRISPR construct facilitates preselection of genome-edited and transgene-free plants by monitoring the seed fluorescence under the epifluorescent microscope. The protocol provides the detailed information about all steps required to perform genome editing and to obtain loss-of-function mutants in different Arabidopsis accessions within merely two generations.
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Affiliation(s)
- Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Longfei Zhu
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
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19
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Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. BIOLOGY 2021; 10:biology10080771. [PMID: 34440003 PMCID: PMC8389541 DOI: 10.3390/biology10080771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Simple Summary The selection of varieties more resilient to disease and climate change requires generating new genetic diversity for breeding. The main mechanism for reshuffling genetic information is through the recombination of chromosomes during meiosis. We showed in oilseed rape (Brassica napus, AACC, 2n = 4x = 38), which is a natural hybrid formed from a cross between turnip (B. rapa, AA, 2n = 2x = 20) and cabbage (B. oleracea, CC, 2n = 2x = 18), that there is significantly more crossovers occurring along the entire A chromosomes in allotriploid AAC (crossbetween B. napus and B. rapa) than in diploid AA or allotetraploid AACC hybrids. We demonstrated that these allotriploid AAC hybrids are highly efficient to introduce new variability within oilseed rape varieties, notably by enabling the introduction of small genomic regions carrying genes controlling agronomically interesting traits. Abstract Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Coleen Tanguy
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Maryse Lodé-Taburel
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Régine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Mathieu Rousseau-Gueutin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France; (F.B.); (A.P.); (C.T.); (G.T.); (F.E.); (L.M.); (M.G.); (M.L.-T.); (V.H.); (J.M.); (O.C.); (C.F.); (R.D.); (M.R.-G.)
- Correspondence: ; Tel.: +33-2-23-48-51-31
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Kuo P, Da Ines O, Lambing C. Rewiring Meiosis for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:708948. [PMID: 34349775 PMCID: PMC8328115 DOI: 10.3389/fpls.2021.708948] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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