1
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Blaschek L. Playing the field: The molecular basis of fruit morphology-based bet-hedging. THE PLANT CELL 2024; 36:2451-2452. [PMID: 38620060 PMCID: PMC11218761 DOI: 10.1093/plcell/koae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Affiliation(s)
- Leonard Blaschek
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Department of Plant & Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
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2
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Kong S, Zhu M, Roeder AHK. Self-organization underlies developmental robustness in plants. Cells Dev 2024:203936. [PMID: 38960068 DOI: 10.1016/j.cdev.2024.203936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Development is a self-organized process that builds on cells and their interactions. Cells are heterogeneous in gene expression, growth, and division; yet how development is robust despite such heterogeneity is a fascinating question. Here, we review recent progress on this topic, highlighting how developmental robustness is achieved through self-organization. We will first discuss sources of heterogeneity, including stochastic gene expression, heterogeneity in growth rate and direction, and heterogeneity in division rate and precision. We then discuss cellular mechanisms that buffer against such noise, including Paf1C- and miRNA-mediated denoising, spatiotemporal growth averaging and compensation, mechanisms to improve cell division precision, and coordination of growth rate and developmental timing between different parts of an organ. We also discuss cases where such heterogeneity is not buffered but utilized for development. Finally, we highlight potential directions for future studies of noise and developmental robustness.
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Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mingyuan Zhu
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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3
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Sajeev N, Koornneef M, Bentsink L. A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination. THE PLANT CELL 2024; 36:1358-1376. [PMID: 38215009 PMCID: PMC11062444 DOI: 10.1093/plcell/koad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.
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Affiliation(s)
- Nikita Sajeev
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6708PB Wageningen, the Netherlands
- Max Planck Institute for Plant Breeding Research, Former Department of Plant Breeding and Genetics, Koeln 50829, Germany
| | - Leónie Bentsink
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
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4
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Abley K, Goswami R, Locke JCW. Bet-hedging and variability in plant development: seed germination and beyond. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230048. [PMID: 38432313 PMCID: PMC10909506 DOI: 10.1098/rstb.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/28/2023] [Indexed: 03/05/2024] Open
Abstract
When future conditions are unpredictable, bet-hedging strategies can be advantageous. This can involve isogenic individuals producing different phenotypes, under the same environmental conditions. Ecological studies provide evidence that variability in seed germination time has been selected for as a bet-hedging strategy. We demonstrate how variability in germination time found in Arabidopsis could function as a bet-hedging strategy in the face of unpredictable lethal stresses. Despite a body of knowledge on how the degree of seed dormancy versus germination is controlled, relatively little is known about how differences between isogenic seeds in a batch are generated. We review proposed mechanisms for generating variability in germination time and the current limitations and new possibilities for testing the model predictions. We then look beyond germination to the role of variability in seedling and adult plant growth and review new technologies for quantification of noisy gene expression dynamics. We discuss evidence for phenotypic variability in plant traits beyond germination being under genetic control and propose that variability in stress response gene expression could function as a bet-hedging strategy. We discuss open questions about how noisy gene expression could lead to between-plant heterogeneity in gene expression and phenotypes. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Katie Abley
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
| | - Rituparna Goswami
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
| | - James C. W. Locke
- The Sainsbury Laboratory, University of Cambridge, Cambridge, Cambridgeshire CB2 1LR, UK
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5
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Ohlsson JA, Leong JX, Elander PH, Ballhaus F, Holla S, Dauphinee AN, Johansson J, Lommel M, Hofmann G, Betnér S, Sandgren M, Schumacher K, Bozhkov PV, Minina EA. SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:584-600. [PMID: 38141174 DOI: 10.1111/tpj.16587] [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: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.
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Affiliation(s)
- Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Jia Xuan Leong
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, D-72076, Germany
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Florentine Ballhaus
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | | | - Mark Lommel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Microbiology, Saarland University, Campus A1.5, Saarbrücken, 66123, Germany
| | - Gero Hofmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Staffan Betnér
- Northern Registry Centre, Department of Public Health and Clinical Medicine, Umeå University, Umeå, 90187, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Karin Schumacher
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
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6
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Krzyszton M, Sacharowski SP, Manjunath VH, Muter K, Bokota G, Wang C, Plewczyński D, Dobisova T, Swiezewski S. Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size. PLANT COMMUNICATIONS 2024; 5:100732. [PMID: 37828740 PMCID: PMC10873894 DOI: 10.1016/j.xplc.2023.100732] [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: 07/21/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous seeds. Using automated phenotype analysis, we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large seeds. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds have higher expression of translation-related genes implicated in germination competence. By contrast, small seeds have elevated expression of many positive regulators of dormancy, including a key regulator of this process, the DOG1 gene. Differences in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms; in small seeds, the proximal poly(A) site is selected, resulting in a short mRNA isoform. Furthermore, single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single-seed level, expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
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Affiliation(s)
- Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland.
| | - Sebastian P Sacharowski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland
| | - Veena Halale Manjunath
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland
| | - Katarzyna Muter
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland
| | - Grzegorz Bokota
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ce Wang
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland
| | - Dariusz Plewczyński
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland; Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Poland.
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7
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Alexandre CM, Bubb KL, Schultz KM, Lempe J, Cuperus JT, Queitsch C. LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 241:253-266. [PMID: 37865885 PMCID: PMC10843042 DOI: 10.1111/nph.19334] [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: 06/05/2023] [Accepted: 09/26/2023] [Indexed: 10/23/2023]
Abstract
Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LIPID TRANSFER PROTEIN 2 (LTP2) greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild-type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.
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Affiliation(s)
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Karla M Schultz
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany 1099
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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8
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Sinha N, Zahra T, Gahane AY, Rout B, Bhattacharya A, Basu S, Chakrabarti A, Thakur AK. Protein reservoirs of seeds are amyloid composites employed differentially for germination and seedling emergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:329-346. [PMID: 37675599 DOI: 10.1111/tpj.16429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/15/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Seed protein localization in seed storage protein bodies (SSPB) and their significance in germination are well recognized. SSPB are spherical and contain an assembly of water-soluble and salt-soluble proteins. Although the native structures of some SSPB proteins are explored, their structural arrangement to the functional correlation in SSPB remains unknown. SSPB are morphologically analogous to electron-dense amyloid-containing structures reported in other organisms. Here, we show that wheat, mungbean, barley, and chickpea SSPB exhibit a speckled pattern of amyloids interspersed in an amyloid-like matrix along with native structures, suggesting the composite nature of SSPB. This is confirmed by multispectral imaging methods, electron microscopy, infrared, and X-ray diffraction analysis, using in situ tissue sections, ex vivo protoplasts, and in vitro SSPB. Laser capture microdissection coupled with peptide fingerprinting has shown that globulin 1 and 3 in wheat, and 8S globulin and conglycinin in mungbean are the major amyloidogenic proteins. The amyloid composites undergo a sustained degradation during germination and seedling growth, facilitated by an intricate interplay of plant hormones and proteases. These results would lay down the foundation for understanding the amyloid composite structure during SSPB biogenesis and its evolution across the plant kingdom and have implications in both basic and applied plant biology.
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Affiliation(s)
- Nabodita Sinha
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Talat Zahra
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Avinash Yashwant Gahane
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Bandita Rout
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | | | | | | | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
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9
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Alexandre CM, Bubb KL, Schultz KM, Lempe J, Cuperus JT, Queitsch C. LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540469. [PMID: 37214854 PMCID: PMC10197655 DOI: 10.1101/2023.05.11.540469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LTP2 greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs, and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.
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Affiliation(s)
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Karla M Schultz
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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10
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Zhou Y, Zhao C, Du T, Li A, Qin Z, Zhang L, Dong S, Wang Q, Hou F. Overexpression of 9- cis-Epoxycarotenoid Dioxygenase Gene, IbNCED1, Negatively Regulates Plant Height in Transgenic Sweet Potato. Int J Mol Sci 2023; 24:10421. [PMID: 37445599 DOI: 10.3390/ijms241310421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Plant height is one of the key agronomic traits for improving the yield of sweet potato. Phytohormones, especially gibberellins (GAs), are crucial to regulate plant height. The enzyme 9-cis-epoxycarotenoid dioxygenase (NCED) is the key enzyme for abscisic acid (ABA) biosynthesis signalling in higher plants. However, its role in regulating plant height has not been reported to date. Here, we cloned a new NCED gene, IbNCED1, from the sweet potato cultivar Jishu26. This gene encoded the 587-amino acid polypeptide containing an NCED superfamily domain. The expression level of IbNCED1 was highest in the stem and the old tissues in the in vitro-grown and field-grown Jishu26, respectively. The expression of IbNCED1 was induced by ABA and GA3. Overexpression of IbNCED1 promoted the accumulation of ABA and inhibited the content of active GA3 and plant height and affected the expression levels of genes involved in the GA metabolic pathway. Exogenous application of GA3 could rescue the dwarf phenotype. In conclusion, we suggest that IbNCED1 regulates plant height and development by controlling the ABA and GA signalling pathways in transgenic sweet potato.
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Affiliation(s)
- Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunling Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Taifeng Du
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shunxu Dong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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11
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Wang QY, Yang L, Ge N, Jia JS, Huang RM, Chen C, Meng ZG, Li LG, Chen JW. Exogenous abscisic acid prolongs the dormancy of recalcitrant seed of Panax notoginseng. FRONTIERS IN PLANT SCIENCE 2023; 14:1054736. [PMID: 36866363 PMCID: PMC9971733 DOI: 10.3389/fpls.2023.1054736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/20/2023] [Indexed: 06/12/2023]
Abstract
The seeds of Panax notoginseng (Burk.) F. H. Chen are typically characterized by their recalcitrance and after-ripening process and exhibit a high water content at harvest as well as a high susceptibility to dehydration. Storage difficulty and the low germination of recalcitrant seeds of P. notoginseng are known to cause an obstacle to agricultural production. In this study, the ratio of embryo to endosperm (Em/En) in abscisic acid (ABA) treatments (1 mg·l-1 and 10 mg·l-1, LA and HA) was 53.64% and 52.34%, respectively, which were lower than those in control check (CK) (61.98%) at 30 days of the after-ripening process (DAR). A total of 83.67% of seeds germinated in the CK, 49% of seeds germinated in the LA treatment, and 37.33% of seeds germinated in the HA treatment at 60 DAR. The ABA, gibberellin (GA), and auxin (IAA) levels were increased in the HA treatment at 0 DAR, while the jasmonic acid (JA) levels were decreased. ABA, IAA, and JA were increased, but GA was decreased with HA treatment at 30 DAR. A total of 4,742, 16,531, and 890 differentially expressed genes (DEGs) were identified between the HA-treated and CK groups, respectively, along with obvious enrichment in the ABA-regulated plant hormone pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The expression of pyracbactin resistance-like (PYL) and SNF1-related protein kinase subfamily 2 (SnRK2s) increased in the ABA-treated groups, whereas the expression of type 2C protein phosphatase (PP2C) decreased, both of which are related to the ABA signaling pathway. As a result of the changes in expression of these genes, increased ABA signaling and suppressed GA signaling could inhibit the growth of the embryo and the expansion of developmental space. Furthermore, our results demonstrated that MAPK signaling cascades might be involved in the amplification of hormone signaling. Meanwhile, our study uncovered that the exogenous hormone ABA could inhibit embryonic development, promote dormancy, and delay germination in recalcitrant seeds. These findings reveal the critical role of ABA in regulating the dormancy of recalcitrant seeds, and thereby provide a new insight into recalcitrant seeds in agricultural production and storage.
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Affiliation(s)
- Qing-Yan Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Ling Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Na Ge
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Jin-Shan Jia
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Rong-Mei Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Cui Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Zhen-Gui Meng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Long-Gen Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
| | - Jun-Wen Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China
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Regain flood adaptation in rice through a 14-3-3 protein OsGF14h. Nat Commun 2022; 13:5664. [PMID: 36175427 PMCID: PMC9522936 DOI: 10.1038/s41467-022-33320-x] [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: 08/30/2021] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Contemporary climatic stress seriously affects rice production. Unfortunately, long-term domestication and improvement modified the phytohormones network to achieve the production needs of cultivated rice, thus leading to a decrease in adaptation. Here, we identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance. OsGF14h acts as a signal switch to balance ABA signaling and GA biosynthesis by interacting with the transcription factors OsHOX3 and OsVP1, thereby boosting the seeding rate from 13.5% to 60.5% for anaerobic sensitive variety under flooded direct-seeded conditions. Meanwhile, OsGF14h co-inheritance with the Rc (red pericarp gene) promotes divergence between temperate japonica cultivated rice and temperate japonica weedy rice through artificial and natural selection. Our study retrieves a superior allele that has been lost during modern japonica rice improvement and provides a fine-tuning tool to improve flood adaptation for elite rice varieties. Waterlogging tolerance is important in direct seeding rice cultivation practice. Here, the authors identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance by balancing ABA signaling and GA biosynthesis.
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13
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Krzyszton M, Yatusevich R, Wrona M, Sacharowski SP, Adamska D, Swiezewski S. Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction. PLANT PHYSIOLOGY 2022; 190:211-225. [PMID: 35670742 PMCID: PMC9438484 DOI: 10.1093/plphys/kiac265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Seeds are highly resilient to the external environment, which allows plants to persist in unpredictable and unfavorable conditions. Some plant species have adopted a bet-hedging strategy to germinate a variable fraction of seeds in any given condition, and this could be explained by population-based threshold models. Here, in the model plant Arabidopsis (Arabidopsis thaliana), we induced secondary dormancy (SD) to address the transcriptional heterogeneity among seeds that leads to binary germination/nongermination outcomes. We developed a single-seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1) showed a shift toward higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single-seed transcriptomes during SD-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single-seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.
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Affiliation(s)
| | | | - Magdalena Wrona
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw 02-106, Poland
| | - Sebastian P Sacharowski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw 02-106, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
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Martínez-Berdeja A. Variation in dormancy and the timing of germination allows annuals to display different winter life histories in contrasting seasonal environments. A commentary on: 'Effects of primary seed dormancy on lifetime fitness of Arabidopsis thaliana in the field'. ANNALS OF BOTANY 2022; 129:viii-x. [PMID: 35349632 PMCID: PMC9292594 DOI: 10.1093/aob/mcac034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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15
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Bagautdinova ZZ, Omelyanchuk N, Tyapkin AV, Kovrizhnykh VV, Lavrekha VV, Zemlyanskaya EV. Salicylic Acid in Root Growth and Development. Int J Mol Sci 2022; 23:ijms23042228. [PMID: 35216343 PMCID: PMC8875895 DOI: 10.3390/ijms23042228] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.
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Affiliation(s)
- Zulfira Z. Bagautdinova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Nadya Omelyanchuk
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Aleksandr V. Tyapkin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vasilina V. Kovrizhnykh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Viktoriya V. Lavrekha
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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16
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Abley K, Formosa-Jordan P, Tavares H, Chan EY, Afsharinafar M, Leyser O, Locke JC. An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time. eLife 2021; 10:59485. [PMID: 34059197 PMCID: PMC8169117 DOI: 10.7554/elife.59485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/01/2021] [Indexed: 12/31/2022] Open
Abstract
Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability and its underlying mechanisms. We show extensive variation in seed germination time variability between Arabidopsis accessions and use a multiparent recombinant inbred population to identify two genetic loci involved in this trait. Both loci include genes implicated in modulating abscisic acid (ABA) sensitivity. Mutually antagonistic regulation between ABA, which represses germination, and gibberellic acid (GA), which promotes germination, underlies the decision to germinate and can act as a bistable switch. A simple stochastic model of the ABA-GA network shows that modulating ABA sensitivity can generate the range of germination time distributions we observe experimentally. We validate the model by testing its predictions on the effects of exogenous hormone addition. Our work provides a foundation for understanding the mechanism and functional role of phenotypic variability in germination time.
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Affiliation(s)
- Katie Abley
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Pau Formosa-Jordan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Emily Yt Chan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Mana Afsharinafar
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ottoline Leyser
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - James Cw Locke
- The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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Gianella M, Bradford KJ, Guzzon F. Ecological, (epi)genetic and physiological aspects of bet-hedging in angiosperms. PLANT REPRODUCTION 2021; 34:21-36. [PMID: 33449209 PMCID: PMC7902588 DOI: 10.1007/s00497-020-00402-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/28/2020] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Bet-hedging is a complex evolutionary strategy involving morphological, eco-physiological, (epi)genetic and population dynamics aspects. We review these aspects in flowering plants and propose further research needed for this topic. Bet-hedging is an evolutionary strategy that reduces the temporal variance in fitness at the expense of a lowered arithmetic mean fitness. It has evolved in organisms subjected to variable cues from the external environment, be they abiotic or biotic stresses such as irregular rainfall or predation. In flowering plants, bet-hedging is exhibited by hundreds of species and is mainly exerted by reproductive organs, in particular seeds but also embryos and fruits. The main example of bet-hedging in angiosperms is diaspore heteromorphism in which the same individual produces different seed/fruit morphs in terms of morphology, dormancy, eco-physiology and/or tolerance to biotic and abiotic stresses in order to 'hedge its bets' in unpredictable environments. The objective of this review is to provide a comprehensive overview of the ecological, genetic, epigenetic and physiological aspects involved in shaping bet-hedging strategies, and how these can affect population dynamics. We identify several open research questions about bet-hedging strategies in plants: 1) understanding ecological trade-offs among different traits; 2) producing more comprehensive phylogenetic analyses to understand the diffusion and evolutionary implications of this strategy; 3) clarifying epigenetic mechanisms related to bet-hedging and plant responses to environmental cues; and 4) applying multi-omics approaches to study bet-hedging at different levels of detail. Clarifying those aspects of bet-hedging will deepen our understanding of this fascinating evolutionary strategy.
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Affiliation(s)
- Maraeva Gianella
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Kent J Bradford
- Department of Plant Sciences, Seed Biotechnology Center, University of California, Davis, USA
| | - Filippo Guzzon
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, Mexico State, Mexico.
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