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Laitinen RAE, Nikoloski Z. Strategies to identify and dissect trade-offs in plants. Mol Ecol 2024; 33:e16780. [PMID: 36380694 DOI: 10.1111/mec.16780] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) experimental designed used (i.e. a single individual across different environments or a population of individuals in single or multiple environments). We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.
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Affiliation(s)
- Roosa A E Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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2
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Sageman-Furnas K, Duarte GT, Laitinen RAE. Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of Arabidopsis thaliana. Plant Cell Physiol 2024; 65:420-427. [PMID: 38153761 PMCID: PMC11020215 DOI: 10.1093/pcp/pcad167] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Shoot growth directly impacts plant productivity. Plants adjust their shoot growth in response to varying environments to maximize resource capture and stress resilience. While several factors controlling shoot growth are known, the complexity of the regulation and the input of the environment are not fully understood. We have investigated shoot growth repression induced by low ambient temperatures in hybrids of Arabidopsis thaliana Kro-0 and BG-5 accessions. To continue our previous studies, we confirmed that the Kro-0 allele of DYNAMIN-RELATED PROTEIN 3B causes stunted shoot growth in the BG-5 background. We also found that shoot growth repression was most pronounced near the apex at a lower temperature and that the cells in the hybrid stem failed to elongate correctly. Furthermore, we observed that shoot growth repression in hybrids depended on light availability. Global gene expression analysis indicated the involvement of hormones, especially strigolactone, associated with the dwarf phenotype. Altogether, this study enhances our knowledge on the genetic, physiological and environmental factors associated with shoot growth regulation.
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Affiliation(s)
- Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Department of Biology, Duke University, Durham, NC 27008, USA
| | - Gustavo T Duarte
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Belgian Nuclear Research Centre (SCK CEN), Unit for Biosphere Impact Studies, Boeretang 200, Mol 2400, Belgium
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00014, Finland
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3
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Laitinen RAE. Importance of phenotypic plasticity in crop resilience. J Exp Bot 2024; 75:670-673. [PMID: 38307517 PMCID: PMC10837008 DOI: 10.1093/jxb/erad465] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
This article comments on:
Guo T, Wei J, Li X, Yu J. 2024. Environmental context of phenotypic plasticity in flowering time in sorghum and rice. Journal of Experimental Botany 75, 1004–1015.
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Affiliation(s)
- Roosa A E Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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4
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Tong H, Laitinen RAE, Nikoloski Z. Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. New Phytol 2023; 240:426-438. [PMID: 37507350 DOI: 10.1111/nph.19154] [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] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023]
Abstract
Plants can rapidly mitigate the effects of suboptimal growth environments by phenotypic plasticity of fitness-traits. While genetic variation for phenotypic plasticity offers the means for breeding climate-resilient crop lines, accurate genomic prediction models for plasticity of fitness-related traits are still lacking. Here, we employed condition- and accession-specific metabolic models for 67 Arabidopsis thaliana accessions to dissect and predict plasticity of rosette growth to changes in nitrogen availability. We showed that specific reactions in photorespiration, linking carbon and nitrogen metabolism, as well as key pathways of central carbon metabolism exhibited substantial genetic variation for flux plasticity. We also demonstrated that, in comparison with a genomic prediction model for fresh weight (FW), genomic prediction of growth plasticity improves the predictability of FW under low nitrogen by 58.9% and by additional 15.4% when further integrating data on plasticity of metabolic fluxes. Therefore, the combination of metabolic and statistical modeling provides a stepping stone in understanding the molecular mechanisms and improving the predictability of plasticity for fitness-related traits.
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Affiliation(s)
- Hao Tong
- Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Roosa A E Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Zoran Nikoloski
- Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
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5
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Andreou GM, Messer M, Tong H, Nikoloski Z, Laitinen RAE. Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana. Quant Plant Biol 2023; 4:e4. [PMID: 37077703 PMCID: PMC10095859 DOI: 10.1017/qpb.2023.3] [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: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 05/03/2023]
Abstract
Phenotypic plasticity is a heritable trait that provides sessile organisms a strategy to rapidly mitigate negative effects of environmental change. Yet, we have little understanding of the mode of inheritance and genetic architecture of plasticity in different focal traits relevant to agricultural applications. This study builds on our recent discovery of genes controlling temperature-mediated flower size plasticity in Arabidopsis thaliana and focuses on dissecting the mode of inheritance and combining ability of plasticity in the context of plant breeding. We created a full diallel cross using 12 A. thaliana accessions displaying different temperature-mediated flower size plasticities, scored as the fold change between two temperatures. Griffing's analysis of variance in flower size plasticity indicated that non-additive genetic action shapes this trait and pointed at challenges and opportunities when breeding for reduced plasticity. Our findings provide an outlook of flower size plasticity that is important for developing resilient crops for future climates.
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Affiliation(s)
- Gregory M. Andreou
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Michaela Messer
- Molecular Mechanisms of Plant Adaptation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Hao Tong
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Roosa A. E. Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Molecular Mechanisms of Plant Adaptation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Author for correspondence: Roosa A. E. Laitinen, E-mail:
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6
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Sageman-Furnas K, Nurmi M, Contag M, Plötner B, Alseekh S, Wiszniewski A, Fernie AR, Smith LM, Laitinen RAE. A. thaliana Hybrids Develop Growth Abnormalities through Integration of Stress, Hormone and Growth Signaling. Plant Cell Physiol 2022; 63:944-954. [PMID: 35460255 PMCID: PMC9282726 DOI: 10.1093/pcp/pcac056] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Hybrids between Arabidopsis thaliana accessions are important in revealing the consequences of epistatic interactions in plants. F1 hybrids between the A. thaliana accessions displaying either defense or developmental phenotypes have been revealing the roles of the underlying epistatic genes. The interaction of two naturally occurring alleles of the OUTGROWTH-ASSOCIATED KINASE (OAK) gene in Sha and Lag2-2, previously shown to cause a similar phenotype in a different allelic combination in A. thaliana, was required for the hybrid phenotype. Outgrowth formation in the hybrids was associated with reduced levels of salicylic acid, jasmonic acid and abscisic acid in petioles and the application of these hormones mitigated the formation of the outgrowths. Moreover, different abiotic stresses were found to mitigate the outgrowth phenotype. The involvement of stress and hormone signaling in outgrowth formation was supported by a global transcriptome analysis, which additionally revealed that TCP1, a transcription factor known to regulate leaf growth and symmetry, was downregulated in the outgrowth tissue. These results demonstrate that a combination of natural alleles of OAK regulates growth and development through the integration of hormone and stress signals and highlight the importance of natural variation as a resource to discover the function of gene variants that are not present in the most studied accessions of A. thaliana.
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Affiliation(s)
- Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Meike Contag
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Lisa M Smith
- School of Biosciences and Institute for Sustainable Food, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Duarte GT, Pandey PK, Vaid N, Alseekh S, Fernie AR, Nikoloski Z, Laitinen RAE. Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. Plant Cell Environ 2021; 44:3398-3411. [PMID: 34228823 DOI: 10.1111/pce.14146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/13/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 05/12/2023]
Abstract
Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.
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Affiliation(s)
- Gustavo Turqueto Duarte
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Prashant K Pandey
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- National Research Council Canada (NRC-CNRC), Aquatic and Crop Resource Development (ACRD), Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Saleh Alseekh
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology, Plovdiv, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Roosa A E Laitinen
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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8
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Vaid N, Ishihara H, Plötner B, Sageman-Furnas K, Wiszniewski A, Laitinen RAE. Leaf chlorosis in Arabidopsis thaliana hybrids is associated with transgenerational decline and imbalanced ribosome number. New Phytol 2020; 228:989-1000. [PMID: 32557724 DOI: 10.1111/nph.16752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 05/09/2023]
Abstract
The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD-box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this study, we use a sophisticated genetic approach to investigate genes underlying hybrid chlorosis. Sequence comparisons, DNA methylation inhibitor drug treatment and segregation analysis were used to investigate the epigenetic regulation of hybrid chlorosis. Relative rRNA numbers were quantified using real-time quantitative PCR. We confirmed the causality of AtRH18 and provided evidence for the involvement of the promoter region of AtRH18 in the hybrid chlorosis. Furthermore, AtMOM1 from the second parent was identified as the likely candidate gene on chromosome 1. Chlorotic hybrids displayed transgenerational decline in chlorosis, and DNA demethylation experiment restored chlorophyll levels in chlorotic hybrids. Quantification of rRNA indicated that hybrid chlorosis was associated with an imbalance in the ratio of cytosolic and plastid ribosomes. Our findings highlight that the epigenetic regulation of AtRH18 causes hybrid breakdown and provide novel information about the role of AtRH18 in plant development.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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9
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Pandey PK, Yu J, Omranian N, Alseekh S, Vaid N, Fernie AR, Nikoloski Z, Laitinen RAE. Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations. Plant Direct 2019; 3:e00186. [PMID: 31799492 PMCID: PMC6884650 DOI: 10.1002/pld3.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 05/26/2023]
Abstract
Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.
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Affiliation(s)
| | - Jing Yu
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | | | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- BioinformaticsInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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10
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Abstract
The ability of an organism to change its phenotype in response to different environments, termed plasticity, is a particularly important characteristic to enable sessile plants to adapt to rapid changes in their surroundings. Plasticity is a quantitative trait that can provide a fitness advantage and mitigate negative effects due to environmental perturbations. Yet, its genetic basis is not fully understood. Alongside technological limitations, the main challenge in studying plasticity has been the selection of suitable approaches for quantification of phenotypic plasticity. Here, we propose a categorization of the existing quantitative measures of phenotypic plasticity into nominal and relative approaches. Moreover, we highlight the recent advances in the understanding of the genetic architecture underlying phenotypic plasticity in plants. We identify four pillars for future research to uncover the genetic basis of phenotypic plasticity, with emphasis on development of computational approaches and theories. These developments will allow us to perform specific experiments to validate the causal genes for plasticity and to discover their role in plant fitness and evolution.
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Affiliation(s)
- Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam, Germany
- Bioinformatics group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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11
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Vaid N, Laitinen RAE. Diverse paths to hybrid incompatibility in Arabidopsis. Plant J 2019; 97:199-213. [PMID: 30098060 DOI: 10.1111/tpj.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 06/25/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 05/28/2023]
Abstract
One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high-throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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12
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Alhajturki D, Muralidharan S, Nurmi M, Rowan BA, Lunn JE, Boldt H, Salem MA, Alseekh S, Jorzig C, Feil R, Giavalisco P, Fernie AR, Weigel D, Laitinen RAE. Dose-dependent interactions between two loci trigger altered shoot growth in BG-5 × Krotzenburg-0 (Kro-0) hybrids of Arabidopsis thaliana. New Phytol 2018; 217:392-406. [PMID: 28906562 DOI: 10.1111/nph.14781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 02/14/2017] [Accepted: 08/06/2017] [Indexed: 06/07/2023]
Abstract
Hybrids occasionally exhibit genetic interactions resulting in reduced fitness in comparison to their parents. Studies of Arabidopsis thaliana have highlighted the role of immune conflicts, but less is known about the role of other factors in hybrid incompatibility in plants. Here, we present a new hybrid incompatibility phenomenon in this species. We have characterized a new case of F1 hybrid incompatibility from a cross between the A. thaliana accessions Krotzenburg-0 (Kro-0) and BG-5, by conducting transcript, metabolite and hormone analyses, and identified the causal loci through genetic mapping. The F1 hybrids showed arrested growth of the main stem, altered shoot architecture, and altered concentrations of hormones in comparison to parents. The F1 phenotype could be rescued in a developmental-stage-dependent manner by shifting to a higher growth temperature. These F1 phenotypes were linked to two loci, one on chromosome 2 and one on chromosome 3. The F2 generation segregated plants with more severe phenotypes which were linked to the same loci as those in the F1 . This study provides novel insights into how previously unknown mechanisms controlling shoot branching and stem growth can result in hybrid incompatibility.
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Affiliation(s)
- Dema Alhajturki
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | | | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Beth A Rowan
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Helena Boldt
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Mohamed A Salem
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Christian Jorzig
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
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13
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Plötner B, Nurmi M, Fischer A, Watanabe M, Schneeberger K, Holm S, Vaid N, Schöttler MA, Walther D, Hoefgen R, Weigel D, Laitinen RAE. Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. Plant J 2017; 91:251-262. [PMID: 28378460 DOI: 10.1111/tpj.13560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 02/15/2017] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 05/28/2023]
Abstract
Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.
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Affiliation(s)
- Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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14
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Świadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, Laitinen RAE. Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana. New Phytol 2017; 213:900-915. [PMID: 27588563 DOI: 10.1111/nph.14155] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/21/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A. thaliana.
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Affiliation(s)
- Magdalena Świadek
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- University of Potsdam, Potsdam, 14476, Germany
| | - Daniela Sieh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Jing Yu
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Marco Todesco
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christian Jorzig
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | | | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Eunyoung Chae
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Florian Schröder
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Sang-Tae Kim
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
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15
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Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, Martín-Pizarro C, Laitinen RAE, Rowan BA, Tenenboim H, Lechner S, Demar M, Habring-Müller A, Lanz C, Rätsch G, Weigel D. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 2014; 159:1341-51. [PMID: 25467443 DOI: 10.1016/j.cell.2014.10.049] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/22/2014] [Accepted: 10/07/2014] [Indexed: 01/07/2023]
Abstract
Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.
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Affiliation(s)
- Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Darya Karelina
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Stephan Ossowski
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Carmen Martín-Pizarro
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Roosa A E Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Hezi Tenenboim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sarah Lechner
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Monika Demar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anette Habring-Müller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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16
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Todesco M, Kim ST, Chae E, Bomblies K, Zaidem M, Smith LM, Weigel D, Laitinen RAE. Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles. PLoS Genet 2014; 10:e1004459. [PMID: 25010663 PMCID: PMC4091793 DOI: 10.1371/journal.pgen.1004459] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/09/2014] [Indexed: 11/23/2022] Open
Abstract
A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to pathogens. Known causes for such autonomous activation of the immune system are hyperactive alleles of immune regulators, or epistatic interactions between immune regulators and unlinked genes. We have discovered a third class, in which the Arabidopsis thaliana immune system is activated by interactions between natural alleles at a single locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these interacting alleles, one of which has evolved recently by partial resurrection of a pseudogene, and each type includes multiple functional variants. Most previously studies hybrid necrosis cases involve rare alleles found in geographically unrelated populations. These two types of ACD6 alleles instead occur at low frequency throughout the range of the species, and have risen to high frequency in the Northeast of Spain, suggesting a role in local adaptation. In addition, such hybrids occur in these populations in the wild. The extensive functional variation among ACD6 alleles points to a central role of this locus in fine-tuning pathogen defenses in natural populations. Plants and their pathogens are engaged in an endless evolutionary battle. The invention of new strategies by pathogens pushes plants to continuously update their defenses. This in turn leads the pathogens to circumvent these new defenses, and so on. Given the abundance of potential enemies, it is therefore not surprising that genes involved in defense against pathogens are among the most variable in plants. A drawback of this extreme variation in pathogen-recognition mechanisms is that at times the plant mistakes itself for an enemy, leading to autonomous activation of defense responses in the absence of pathogens. Conventional models for this phenomenon, called hybrid necrosis, require the interaction between two different genes. Here we show instead that hybrid necrosis can be triggered by interactions between variants of a single gene, ACD6 (ACCELERATED CELL DEATH 6). Several of these variants are common in natural Arabidopsis thaliana populations and can interact to give different levels of activation of the immune system. Our results provide important information into the evolution and operation of the plant defense system. Moreover, the abundant presence of ACD6 functional variation suggests a major role for this gene in modulating plant defenses in nature.
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Affiliation(s)
- Marco Todesco
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
| | - Roosa A. E. Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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17
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Deng X, Bashandy H, Ainasoja M, Kontturi J, Pietiäinen M, Laitinen RAE, Albert VA, Valkonen JPT, Elomaa P, Teeri TH. Functional diversification of duplicated chalcone synthase genes in anthocyanin biosynthesis of Gerbera hybrida. New Phytol 2014; 201:1469-1483. [PMID: 24266452 DOI: 10.1111/nph.12610] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [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: 09/01/2013] [Accepted: 10/17/2013] [Indexed: 05/19/2023]
Abstract
• Chalcone synthase (CHS) is the key enzyme in the first committed step of the flavonoid biosynthetic pathway and catalyzes the stepwise condensation of 4-coumaroyl-CoA and malonyl-CoA to naringenin chalcone. In plants, CHS is often encoded by a small family of genes that are temporally and spatially regulated. Our earlier studies have shown that GCHS4 is highly activated by ectopic expression of an MYB-type regulator GMYB10 in gerbera (Gerbera hybrida). • The tissue- and development-specific expression patterns of three gerbera CHS genes were examined. Virus-induced gene silencing (VIGS) was used to knock down GCHS1 and GCHS4 separately in gerbera inflorescences. • Our data show that GCHS4 is the only CHS encoding gene that is expressed in the cyanidin-pigmented vegetative tissues of gerbera cv Terraregina. GCHS3 expression is pronounced in the pappus bristles of the flowers. Expression of both GCHS1 and GCHS4 is high in the epidermal cells of gerbera petals, but only GCHS1 is contributing to flavonoid biosynthesis. • Gerbera contains a family of three CHS encoding genes showing different spatial and temporal regulation. GCHS4 expression in gerbera petals is regulated post-transcriptionally, at the level of either translation elongation or protein stability.
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Affiliation(s)
- Xianbao Deng
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Hany Bashandy
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
- Department of Genetics, Cairo University, 13 Gamaa St., Giza, 12619, Egypt
| | - Miia Ainasoja
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Juha Kontturi
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Milla Pietiäinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Roosa A E Laitinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Paula Elomaa
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Teemu H Teeri
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
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18
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Salomé PA, Bomblies K, Fitz J, Laitinen RAE, Warthmann N, Yant L, Weigel D. The recombination landscape in Arabidopsis thaliana F2 populations. Heredity (Edinb) 2012; 108:447-55. [PMID: 22072068 PMCID: PMC3313057 DOI: 10.1038/hdy.2011.95] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/29/2011] [Accepted: 08/27/2011] [Indexed: 12/20/2022] Open
Abstract
Recombination during meiosis shapes the complement of alleles segregating in the progeny of hybrids, and has important consequences for phenotypic variation. We examined allele frequencies, as well as crossover (XO) locations and frequencies in over 7000 plants from 17 F(2) populations derived from crosses between 18 Arabidopsis thaliana accessions. We observed segregation distortion between parental alleles in over half of our populations. The potential causes of distortion include variation in seed dormancy and lethal epistatic interactions. Such a high occurrence of distortion was only detected here because of the large sample size of each population and the number of populations characterized. Most plants carry only one or two XOs per chromosome pair, and therefore inherit very large, non-recombined genomic fragments from each parent. Recombination frequencies vary between populations but consistently increase adjacent to the centromeres. Importantly, recombination rates do not correlate with whole-genome sequence differences between parental accessions, suggesting that sequence diversity within A. thaliana does not normally reach levels that are high enough to exert a major influence on the formation of XOs. A global knowledge of the patterns of recombination in F(2) populations is crucial to better understand the segregation of phenotypic traits in hybrids, in the laboratory or in the wild.
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Affiliation(s)
- P A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - K Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - J Fitz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - R A E Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - N Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - L Yant
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - D Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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19
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Laitinen RAE, Ainasoja M, Broholm SK, Teeri TH, Elomaa P. Identification of target genes for a MYB-type anthocyanin regulator in Gerbera hybrida. J Exp Bot 2008; 59:3691-703. [PMID: 18725377 PMCID: PMC2561154 DOI: 10.1093/jxb/ern216] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Genetic modification of the flavonoid pathway has been used to produce novel colours and colour patterns in ornamental plants as well as to modify the nutritional and pharmaceutical properties of food crops. It has been suggested that co-ordinate control of multiple steps of the pathway with the help of regulatory genes would lead to a more predictable control of metabolic flux. Regulation of anthocyanin biosynthesis has been studied in a common ornamental plant, Gerbera hybrida (Asteraceae). An R2R3-type MYB factor, GMYB10, shares high sequence similarity and is phylogenetically grouped together with previously characterized regulators of anthocyanin pigmentation. Ectopic expression of GMYB10 leads to strongly enhanced accumulation of anthocyanin pigments as well as to an altered pigmentation pattern in transgenic gerbera plants. Anthocyanin analysis indicates that GMYB10 specifically induces cyanidin biosynthesis in undifferentiated callus and in vegetative tissues. Furthermore, in floral tissues enhanced pelargonidin production is detected. Microarray analysis using the gerbera 9K cDNA array revealed a highly predicted set of putative target genes for GMYB10 including new gene family members of both early and late biosynthetic genes of the flavonoid pathway. However, completely new candidate targets, such as a serine carboxypeptidase-like gene as well, as two new MYB domain factors, GMYB11 and GMYB12, whose exact function in phenylpropanoid biosynthesis is not clear yet, were also identified.
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Affiliation(s)
| | | | | | | | - Paula Elomaa
- To whom correspondence should be addressed: E-mail:
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20
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Laitinen RAE, Pöllänen E, Teeri TH, Elomaa P, Kotilainen M. Transcriptional analysis of petal organogenesis in Gerbera hybrida. Planta 2007; 226:347-60. [PMID: 17334783 DOI: 10.1007/s00425-007-0486-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 01/26/2007] [Indexed: 05/14/2023]
Abstract
Understanding of the molecular interplay, which determines early steps of flower formation has grown considerably during last years. In contrast, genetic actions responsible for how flower organs acquire their size and shape at later phases of organogenesis are still poorly understood. We have exploited the large and anatomically simple Gerbera (Gerbera hybrida var. Terra regina) ray flower petals to describe transcriptional changes during organogenesis. Gerbera 9 K cDNA microarray was utilized to profile gene expression at six different developmental stages of petal organogenesis, at the earliest stage expansion of petals is starting and at the latest stage petals have reached their final size and shape. Genes potentially participating in petal opening were identified based on the similarity in expression with a known marker gene. Our results showed characteristic sets of genes expressed during the cell division and cell expansion phases of petal development. Interestingly, there was a transition stage during which neither cell division nor cell expansion marker genes were abundantly expressed. Moreover, constitutive expression of late petal specific genes indicates that they participate in petal organogenesis throughout the development and they are not involved in stage specific switch points.
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Affiliation(s)
- Roosa A E Laitinen
- Department of Applied Biology, University of Helsinki, P.O.Box 27, 00014 Helsinki, Finland
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21
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Laitinen RAE, Immanen J, Auvinen P, Rudd S, Alatalo E, Paulin L, Ainasoja M, Kotilainen M, Koskela S, Teeri TH, Elomaa P. Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Res 2005; 15:475-86. [PMID: 15781570 PMCID: PMC1074362 DOI: 10.1101/gr.3043705] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [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: 07/23/2004] [Accepted: 01/04/2005] [Indexed: 11/25/2022]
Abstract
Development of composite inflorescences in the plant family Asteraceae has features that cannot be studied in the traditional model plants for flower development. In Gerbera hybrida, inflorescences are composed of morphologically different types of flowers tightly packed into a flower head (capitulum). Individual floral organs such as pappus bristles (sepals) are developmentally specialized, stamens are aborted in marginal flowers, petals and anthers are fused structures, and ovaries are located inferior to other floral organs. These specific features have made gerbera a rewarding target of comparative studies. Here we report the analysis of a gerbera EST database containing 16,994 cDNA sequences. Comparison of the sequences with all plant peptide sequences revealed 1656 unique sequences for gerbera not identified elsewhere within the plant kingdom. Based on the EST database, we constructed a cDNA microarray containing 9000 probes and have utilized it in identification of flower-specific genes and abundantly expressed marker genes for flower scape, pappus, stamen, and petal development. Our analysis revealed several regulatory genes with putative functions in flower-organ development. We were also able to associate a number of abundantly and specifically expressed genes with flower-organ differentiation. Gerbera is an outcrossing species, for which genetic approaches to gene discovery are not readily amenable. However, reverse genetics with the help of gene transfer has been very informative. We demonstrate here the usability of the gerbera microarray as a reliable new tool for identifying novel genes related to specific biological questions and for large-scale gene expression analysis.
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Affiliation(s)
- Roosa A E Laitinen
- Department of Applied Biology, FIN-00014 University of Helsinki, Helsinki, Finland
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22
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Elomaa P, Uimari A, Mehto M, Albert VA, Laitinen RAE, Teeri TH. Activation of anthocyanin biosynthesis in Gerbera hybrida (Asteraceae) suggests conserved protein-protein and protein-promoter interactions between the anciently diverged monocots and eudicots. Plant Physiol 2003; 133:1831-42. [PMID: 14605235 PMCID: PMC300736 DOI: 10.1104/pp.103.026039] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2003] [Revised: 05/20/2003] [Accepted: 09/07/2003] [Indexed: 05/18/2023]
Abstract
We have identified an R2R3-type MYB factor, GMYB10, from Gerbera hybrida (Asteraceae) that shares high sequence homology to and is phylogenetically grouped together with the previously characterized regulators of anthocyanin pigmentation in petunia (Petunia hybrida) and Arabidopsis. GMYB10 is able to induce anthocyanin pigmentation in transgenic tobacco (Nicotiana tabacum), especially in vegetative parts and anthers. In G. hybrida, GMYB10 is involved in activation of anthocyanin biosynthesis in leaves, floral stems, and flowers. In flowers, its expression is restricted to petal epidermal cell layers in correlation with the anthocyanin accumulation pattern. We have shown, using yeast (Saccharomyces cerevisiae) two-hybrid assay, that GMYB10 interacts with the previously isolated bHLH factor GMYC1. Particle bombardment analysis was used to show that GMYB10 is required for activation of a late anthocyanin biosynthetic gene promoter, PGDFR2. cis-Analysis of the target PGDFR2 revealed a sequence element with a key role in activation by GMYB10/GMYC1. This element shares high homology with the anthocyanin regulatory elements characterized in maize (Zea mays) anthocyanin promoters, suggesting that the regulatory mechanisms involved in activation of anthocyanin biosynthesis have been conserved for over 125 million years not only at the level of transcriptional regulators but also at the level of the biosynthetic gene promoters.
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Affiliation(s)
- Paula Elomaa
- Department of Applied Biology, PO Box 27, University of Helsinki, Helsinki FIN-00014, Finland.
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