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Waterworth W, Balobaid A, West C. Seed longevity and genome damage. Biosci Rep 2024; 44:BSR20230809. [PMID: 38324350 PMCID: PMC11111285 DOI: 10.1042/bsr20230809] [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: 11/21/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024] Open
Abstract
Seeds are the mode of propagation for most plant species and form the basis of both agriculture and ecosystems. Desiccation tolerant seeds, representative of most crop species, can survive maturation drying to become metabolically quiescent. The desiccated state prolongs embryo viability and provides protection from adverse environmental conditions, including seasonal periods of drought and freezing often encountered in temperate regions. However, the capacity of the seed to germinate declines over time and culminates in the loss of seed viability. The relationship between environmental conditions (temperature and humidity) and the rate of seed deterioration (ageing) is well defined, but less is known about the biochemical and genetic factors that determine seed longevity. This review will highlight recent advances in our knowledge that provide insight into the cellular stresses and protective mechanisms that promote seed survival, with a focus on the roles of DNA repair and response mechanisms. Collectively, these pathways function to maintain the germination potential of seeds. Understanding the molecular basis of seed longevity provides important new genetic targets for the production of crops with enhanced resilience to changing climates and knowledge important for the preservation of plant germplasm in seedbanks.
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Affiliation(s)
- Wanda Waterworth
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
| | - Atheer Balobaid
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
| | - Chris West
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
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Sano N, Malabarba J, Chen Z, Gaillard S, Windels D, Verdier J. Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:1059493. [PMID: 36507374 PMCID: PMC9729785 DOI: 10.3389/fpls.2022.1059493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.
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Ivanova A, O′Leary B, Signorelli S, Falconet D, Moyankova D, Whelan J, Djilianov D, Murcha MW. Mitochondrial activity and biogenesis during resurrection of Haberlea rhodopensis. THE NEW PHYTOLOGIST 2022; 236:943-957. [PMID: 35872573 PMCID: PMC9804507 DOI: 10.1111/nph.18396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/11/2022] [Indexed: 06/01/2023]
Abstract
Haberlea rhodopensis is a resurrection plant that can tolerate extreme and prolonged periods of desiccation with a rapid restoration of physiological function upon rehydration. Specialized mechanisms are required to minimize cellular damage during desiccation and to maintain integrity for rapid recovery following rehydration. In this study we used respiratory activity measurements, electron microscopy, transcript, protein and blue native-PAGE analysis to investigate mitochondrial activity and biogenesis in fresh, desiccated and rehydrated detached H. rhodopensis leaves. We demonstrate that unlike photosynthesis, mitochondrial respiration was almost immediately activated to levels of fresh tissue upon rehydration. The abundance of transcripts and proteins involved in mitochondrial respiration and biogenesis were at comparable levels in fresh, desiccated and rehydrated tissues. Blue native-PAGE analysis revealed fully assembled and equally abundant OXPHOS complexes in mitochondria isolated from fresh, desiccated and rehydrated detached leaves. We observed a high abundance of alternative respiratory components which correlates with the observed high uncoupled respiration capacity in desiccated tissue. Our study reveals that during desiccation of vascular H. rhodopensis tissue, mitochondrial composition is conserved and maintained at a functional state allowing for an almost immediate activation to full capacity upon rehydration. Mitochondria-specific mechanisms were activated during desiccation which probably play a role in maintaining tolerance.
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Affiliation(s)
- Aneta Ivanova
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - Brendan O′Leary
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- Saskatoon Research and Development Centre, Agriculture and Agri‐Food Canada107 Science PlaceSaskatoonSKK1A 0C5Canada
| | - Santiago Signorelli
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
- Department of Plant Biology, School of AgricultureUniversidad de la RepúblicaE. Garzón 780, Sayago12900MontevideoUruguay
| | - Denis Falconet
- Cell and Plant Physiology Laboratory, CNRS, CEA, INRAE, IRIGUniversité Grenoble Alpes38054GrenobleFrance
| | - Daniela Moyankova
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy BiologyLa Trobe UniversityBundoora3086VICAustralia
| | - Dimitar Djilianov
- AgroBioInstituteAgricultural Academy8 Dragan Tzankov Blvd.1164SofiaBulgaria
| | - Monika W. Murcha
- School of Molecular SciencesThe University of Western Australia35 Stirling Highway, CrawleyPerthWA6009Australia
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Pagano A, Zannino L, Pagano P, Doria E, Dondi D, Macovei A, Biggiogera M, Araújo SDS, Balestrazzi A. Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds. PLANT, CELL & ENVIRONMENT 2022; 45:1457-1473. [PMID: 35188276 PMCID: PMC9311706 DOI: 10.1111/pce.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Paola Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Daniele Dondi
- Department of ChemistryUniversity of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
| | - Susana de Sousa Araújo
- Association BLC3‐Technology and Innovation CampusCentre Bio R&D UnitMacedo de CavaleirosPortugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani'University of PaviaPaviaItaly
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Peng L, Huang X, Qi M, Pritchard HW, Xue H. Mechanistic insights derived from re-establishment of desiccation tolerance in germinating xerophytic seeds: Caragana korshinskii as an example. FRONTIERS IN PLANT SCIENCE 2022; 13:1029997. [PMID: 36420023 PMCID: PMC9677110 DOI: 10.3389/fpls.2022.1029997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 05/13/2023]
Abstract
Germplasm conservation strongly depends on the desiccation tolerance (DT) of seeds. Xerophytic seeds have strong desiccation resistance, which makes them excellent models to study DT. Although some experimental strategies have been applied previously, most methods are difficult to apply to xerophytic seeds. In this review, we attempted to synthesize current strategies for the study of seed DT and provide an in-depth look at Caragana korshinskii as an example. First, we analyze congenital advantages of xerophytes in the study of seed DT. Second, we summarize several strategies used to study DT and illustrate a suitable strategy for xerophytic species. Then, based on our previous studies work with C. korshinskii, a feasible technical strategy for DT re-establishment is provided and we provide illustrate some special molecular mechanisms seen in xerophytic seeds. Finally, several steps to unveil the DT mechanism of xerophytic seeds are suggested, and three scientific questions that the field should consider are listed. We hope to optimize and utilize this strategy for more xerophytic species to more systematically decipher the physiological and molecular processes of seed DT and provide more candidate genes for molecular breeding.
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Affiliation(s)
- Long Peng
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xu Huang
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Manyao Qi
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hugh W. Pritchard
- Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
- Royal Botanic Gardens, Kew, Wakehurst, West Sussex, United Kingdom
| | - Hua Xue
- National Engineering Research Center of Tree breeding and Ecological remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Hua Xue,
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Medicago ABI3 Splicing Isoforms Regulate the Expression of Different Gene Clusters to Orchestrate Seed Maturation. PLANTS 2021; 10:plants10081710. [PMID: 34451755 PMCID: PMC8398556 DOI: 10.3390/plants10081710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Seed maturation comprises important developmental processes, such as seed filling and the acquisition of seed germination capacity, desiccation tolerance, longevity, and dormancy. The molecular regulation of these processes is tightly controlled by the LAFL transcription factors, among which ABSCISIC ACID INSENSITIVE 3 (ABI3) was shown to be involved in most of these seed maturation processes. Here, we studied the ABI3 gene from Medicago truncatula, a model legume plant for seed studies. With the transcriptomes of two loss-of-function Medicago abi3 mutants, we were able to show that many gene classes were impacted by the abi3 mutation at different stages of early, middle, and late seed maturation. We also discovered three MtABI3 expression isoforms, which present contrasting expression patterns during seed development. Moreover, by ectopically expressing these isoforms in Medicago hairy roots generated from the abi3 mutant line background, we showed that each isoform regulated specific gene clusters, suggesting divergent molecular functions. Furthermore, we complemented the Arabidopsis abi3 mutant with each of the three MtABI3 isoforms and concluded that all isoforms were capable of restoring seed viability and desiccation tolerance phenotypes even if not all isoforms complemented the seed color phenotype. Taken together, our results allow a better understanding of the ABI3 network in Medicago during seed development, as well as the discovery of commonly regulated genes from the three MtABI3 isoforms, which can give us new insights into how desiccation tolerance and seed viability are regulated.
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Bizouerne E, Buitink J, Vu BL, Vu JL, Esteban E, Pasha A, Provart N, Verdier J, Leprince O. Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour. BMC PLANT BIOLOGY 2021; 21:124. [PMID: 33648457 PMCID: PMC7923611 DOI: 10.1186/s12870-021-02889-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. RESULTS During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. CONCLUSION The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.
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Affiliation(s)
- Elise Bizouerne
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Julia Buitink
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Benoît Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Joseph Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Eddi Esteban
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jérôme Verdier
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Olivier Leprince
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France.
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Zinsmeister J, Berriri S, Basso DP, Ly-Vu B, Dang TT, Lalanne D, da Silva EAA, Leprince O, Buitink J. The seed-specific heat shock factor A9 regulates the depth of dormancy in Medicago truncatula seeds via ABA signalling. PLANT, CELL & ENVIRONMENT 2020; 43:2508-2522. [PMID: 32683703 DOI: 10.1111/pce.13853] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 05/15/2023]
Abstract
During the later stages of seed maturation, two key adaptive traits are acquired that contribute to seed lifespan and dispersal, longevity and dormancy. The seed-specific heat shock transcription factor A9 is an important hub gene in the transcriptional network of late seed maturation. Here, we demonstrate that HSFA9 plays a role in thermotolerance rather than in ex situ seed conservation. Storage of hsfa9 seeds of Medicago truncatula and Arabidopsis had comparable lifespan at moderate storage relative humidity (RH), whereas at high RH, hsfa9 seeds lost their viability much faster than wild type seeds. Furthermore, we show that in M. truncatula, Mthsfa9 seeds acquired more dormancy during late maturation than wild type. Transient expression of MtHSFA9 in hairy roots and transcriptome analysis of Mthsfa9 Tnt1 insertion mutants identified a deregulation of genes involved in ABA biosynthesis, catabolism and signalling. Consistent with these results, Mthsfa9 seeds exhibited increased ABA levels and higher sensitivity to ABA. These data suggest that in legumes, HSFA9 acts as a negative regulator of the depth of seed dormancy during seed development via the modulation of hormonal balance.
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Affiliation(s)
- Julia Zinsmeister
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Souha Berriri
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Denise Puntel Basso
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
- Departamento de Produção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu, Brazil
| | - Benoit Ly-Vu
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Thi-Thu Dang
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - David Lalanne
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Olivier Leprince
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Julia Buitink
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
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Molecular and environmental factors regulating seed longevity. Biochem J 2020; 477:305-323. [PMID: 31967650 DOI: 10.1042/bcj20190165] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Seed longevity is a central pivot of the preservation of biodiversity, being of main importance to face the challenges linked to global climate change and population growth. This complex, quantitative seed quality trait is acquired on the mother plant during the second part of seed development. Understanding what factors contribute to lifespan is one of the oldest and most challenging questions in plant biology. One of these challenges is to recognize that longevity depends on the storage conditions that are experimentally used because they determine the type and rate of deleterious conditions that lead to cell death and loss of viability. In this review, we will briefly review the different storage methods that accelerate the deteriorative reactions during storage and argue that a minimum amount of information is necessary to interpret the longevity data. Next, we will give an update on recent discoveries on the hormonal factors regulating longevity, both from the ABA signaling pathway but also other hormonal pathways. In addition, we will review the effect of both maternal and abiotic factors that influence longevity. In the last section of this review, we discuss the problems in unraveling cause-effect relationship between the time of death during storage and deteriorative reactions leading to seed ageing. We focus on the three major types of cellular damage, namely membrane permeability, lipid peroxidation and RNA integrity for which germination data on seed stored in dedicated seed banks for long period times are now available.
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Malovichko YV, Shtark OY, Vasileva EN, Nizhnikov AA, Antonets KS. Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea ( Pisum sativum L.). Cells 2020; 9:E779. [PMID: 32210065 PMCID: PMC7140803 DOI: 10.3390/cells9030779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023] Open
Abstract
The garden pea (Pisum sativum L.) is a legume crop of immense economic value. Extensive breeding has led to the emergence of numerous pea varieties, of which some are distinguished by accelerated development in various stages of ontogenesis. One such trait is rapid seed maturation, which, despite novel insights into the genetic control of seed development in legumes, remains poorly studied. This article presents an attempt to dissect mechanisms of early maturation in the pea line Sprint-2 by means of whole transcriptome RNA sequencing in two developmental stages. By using a de novo assembly approach, we have obtained a reference transcriptome of 25,756 non-redundant entries expressed in pea seeds at either 10 or 20 days after pollination. Differential expression in Sprint-2 seeds has affected 13,056 transcripts. A comparison of the two pea lines with a common maturation rate demonstrates that while at 10 days after pollination, Sprint-2 seeds show development retardation linked to intensive photosynthesis, morphogenesis, and cell division, and those at 20 days show a rapid onset of desiccation marked by the cessation of translation and cell anabolism and accumulation of dehydration-protective and -storage moieties. Further inspection of certain transcript functional categories, including the chromatin constituent, transcription regulation, protein turnover, and hormonal regulation, has revealed transcriptomic trends unique to specific stages and cultivars. Among other remarkable features, Sprint-2 demonstrated an enhanced expression of transposable element-associated open reading frames and an altered expression of major maturation regulators and DNA methyltransferase genes. To the best of our knowledge, this is the first comparative transcriptomic study in which the issue of the seed maturation rate is addressed.
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Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Ekaterina N. Vasileva
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelskogo sh., 3, Pushkin, 196608 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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11
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Lyall R, Schlebusch SA, Proctor J, Prag M, Hussey SG, Ingle RA, Illing N. Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1349-1367. [PMID: 31680354 PMCID: PMC7187197 DOI: 10.1111/tpj.14596] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/09/2019] [Accepted: 10/21/2019] [Indexed: 05/25/2023]
Abstract
It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed-specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.
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Affiliation(s)
- Rafe Lyall
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Stephen A. Schlebusch
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Jessica Proctor
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Mayur Prag
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoria0002South Africa
| | - Robert A. Ingle
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Nicola Illing
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
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12
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Jo L, Pelletier JM, Harada JJ. Central role of the LEAFY COTYLEDON1 transcription factor in seed development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:564-580. [PMID: 30916433 DOI: 10.1111/jipb.12806] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/16/2019] [Indexed: 05/04/2023]
Abstract
Seed development is a complex period of the flowering plant life cycle. After fertilization, the three main regions of the seed, embryo, endosperm and seed coat, undergo a series of developmental processes that result in the production of a mature seed that is developmentally arrested, desiccated, and metabolically quiescent. These processes are highly coordinated, both temporally and spatially, to ensure the proper growth and development of the seed. The transcription factor, LEAFY COTYLEDON1 (LEC1), is a central regulator that controls several aspects of embryo and endosperm development, including embryo morphogenesis, photosynthesis, and storage reserve accumulation. Thus, LEC1 regulates distinct sets of genes at different stages of seed development. Despite its critical importance for seed development, an understanding of the mechanisms underlying LEC1's multifunctionality is only beginning to be obtained. Recent studies describe the roles of specific transcription factors and the hormones, gibberellic acid and abscisic acid, in controlling the activity and transcriptional specificity of LEC1 across seed development. Moreover, studies indicate that LEC1 acts as a pioneer transcription factor to promote epigenetic reprogramming during embryogenesis. In this review, we discuss the mechanisms that enable LEC1 to serve as a central regulator of seed development.
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Affiliation(s)
- Leonardo Jo
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
| | - Julie M Pelletier
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
| | - John J Harada
- Department of Plant Biology and Plant Biology Graduate Group, University of California, Davis, USA
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13
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Marques A, Buijs G, Ligterink W, Hilhorst H. Evolutionary ecophysiology of seed desiccation sensitivity. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1083-1095. [PMID: 32290970 DOI: 10.1071/fp18022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/11/2018] [Indexed: 05/28/2023]
Abstract
Desiccation sensitive (DS) seeds do not survive dry storage due to their lack of desiccation tolerance. Almost half of the plant species in tropical rainforests produce DS seeds and therefore the desiccation sensitivity of these seeds represents a problem for and long-term biodiversity conservation. This phenomenon raises questions as to how, where and why DS (desiccation sensitive)-seeded species appeared during evolution. These species evolved probably independently from desiccation tolerant (DT) seeded ancestors. They adapted to environments where the conditions are conducive to immediate germination after shedding, e.g. constant and abundant rainy seasons. These very predictable conditions offered a relaxed selection for desiccation tolerance that eventually got lost in DS seeds. These species are highly dependent on their environment to survive and they are seriously threatened by deforestation and climate change. Understanding of the ecology, evolution and molecular mechanisms associated with seed desiccation tolerance can shed light on the resilience of DS-seeded species and guide conservation efforts. In this review, we survey the available literature for ecological and physiological aspects of DS-seeded species and combine it with recent knowledge obtained from DT model species. This enables us to generate hypotheses concerning the evolution of DS-seeded species and their associated genetic alterations.
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Affiliation(s)
- Alexandre Marques
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Gonda Buijs
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
| | - Henk Hilhorst
- Laboratory of Plant Physiology, Wageningen University and Research, PO Box 16, 6700AA Wageningen, The Netherlands
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14
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Plant Desiccation Tolerance and its Regulation in the Foliage of Resurrection “Flowering-Plant” Species. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080146] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The majority of flowering-plant species can survive complete air-dryness in their seed and/or pollen. Relatively few species (‘resurrection plants’) express this desiccation tolerance in their foliage. Knowledge of the regulation of desiccation tolerance in resurrection plant foliage is reviewed. Elucidation of the regulatory mechanism in resurrection grasses may lead to identification of genes that can improve stress tolerance and yield of major crop species. Well-hydrated leaves of resurrection plants are desiccation-sensitive and the leaves become desiccation tolerant as they are drying. Such drought-induction of desiccation tolerance involves changes in gene-expression causing extensive changes in the complement of proteins and the transition to a highly-stable quiescent state lasting months to years. These changes in gene-expression are regulated by several interacting phytohormones, of which drought-induced abscisic acid (ABA) is particularly important in some species. Treatment with only ABA induces desiccation tolerance in vegetative tissue of Borya constricta Churchill. and Craterostigma plantagineum Hochstetter. but not in the resurrection grass Sporobolus stapfianus Gandoger. Suppression of drought-induced senescence is also important for survival of drying. Further research is needed on the triggering of the induction of desiccation tolerance, on the transition between phases of protein synthesis and on the role of the phytohormone, strigolactone and other potential xylem-messengers during drying and rehydration.
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15
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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16
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iTRAQ-based quantitative proteomic analysis reveals pathways associated with re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. J Proteomics 2018; 179:1-16. [DOI: 10.1016/j.jprot.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
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17
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Le Signor C, Vernoud V, Noguero M, Gallardo K, Thompson RD. Functional Genomics and Seed Development in Medicago truncatula: An Overview. Methods Mol Biol 2018; 1822:175-195. [PMID: 30043305 DOI: 10.1007/978-1-4939-8633-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The study of seed development in the model species Medicago truncatula has made a significant contribution to our understanding of this process in crop legumes. Thanks to the availability of comprehensive proteomics and transcriptomics databases, coupled with exhaustive mutant collections, the roles of several regulatory genes in development and maturation are beginning to be deciphered and functionally validated. Advances in next-generation sequencing and the availability of a genomic sequence have made feasible high-density SNP genotyping, allowing the identification of markers tightly linked to traits of agronomic interest. A further major advance is to be expected from the integration of omics resources in functional network construction, which has been used recently to identify "hub" genes central to important traits.
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Affiliation(s)
- Christine Le Signor
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mélanie Noguero
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Richard D Thompson
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
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18
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Costa MCD, Cooper K, Hilhorst HWM, Farrant JM. Orthodox Seeds and Resurrection Plants: Two of a Kind? PLANT PHYSIOLOGY 2017; 175:589-599. [PMID: 28851758 PMCID: PMC5619911 DOI: 10.1104/pp.17.00760] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/22/2017] [Indexed: 05/27/2023]
Abstract
Understanding shared strategies for desiccation tolerance in orthodox seeds and resurrection plants can yield insights for agricultural improvement.
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Affiliation(s)
- Maria-Cecília D Costa
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
| | - Keren Cooper
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, 7701 Cape Town, South Africa
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19
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Giarola V, Hou Q, Bartels D. Angiosperm Plant Desiccation Tolerance: Hints from Transcriptomics and Genome Sequencing. TRENDS IN PLANT SCIENCE 2017; 22:705-717. [PMID: 28622918 DOI: 10.1016/j.tplants.2017.05.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/12/2017] [Accepted: 05/18/2017] [Indexed: 05/21/2023]
Abstract
Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs. Modification and reshuffling of existing cis-regulatory promoter elements seems to play a role in the rewiring of regulatory networks required for increased expression of DT-related genes in resurrection species.
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Affiliation(s)
- Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Quancan Hou
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany; Present address: Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany.
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20
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Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Young ND, Prosperi JM, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K. Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds. THE NEW PHYTOLOGIST 2017; 214:1597-1613. [PMID: 28322451 DOI: 10.1111/nph.14500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/25/2023]
Abstract
Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop. Key candidates identified include genes involved in transcription, chromatin remodeling, post-translational modifications, transport and targeting of proteins to storage vacuoles. Inference of a gene coexpression network of 12 candidate transcription factors and globulin genes revealed the transcription factor ABA-insensitive 5 (ABI5) as a highly connected hub. Characterization of loss-of-function abi5 mutants in pea uncovered a role for ABI5 in controlling the relative abundance of vicilin, a sulfur-poor 7S globulin, in pea seeds. This demonstrates the feasibility of using genome-wide association studies in M. truncatula to reveal genes that can be modulated to improve seed nutritional value.
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Affiliation(s)
- Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Amandine Bordat
- Unité Mixte de Recherche (UMR) 1332 Biologie du Fruit et Pathologie, INRA, 33882, Villenave d'Ornon, France
| | - Maya Belghazi
- UMR 7286 - CRN2M, Centre d'Analyses Protéomiques de Marseille, CNRS, Aix-Marseille Université, Marseille, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements-Centre National de la Recherche Scientifique (CNRS) UMR 7247-Université François Rabelais-Institut Français du Cheval et de l'Equitation, Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, 37380, Nouzilly, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, INRA, Université de Toulouse, Castanet-Tolosan, France
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Jean-Marie Prosperi
- Genetic Improvement and Adaptation of Mediterranean and Tropical Plants (AGAP), INRA, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier Supagro, 34060, Montpellier, France
| | - Olivier Leprince
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Richard D Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Julia Buitink
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
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21
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Srinivasan A, Jiménez-Gómez JM, Fornara F, Soppe WJJ, Brambilla V. Alternative splicing enhances transcriptome complexity in desiccating seeds. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:947-958. [PMID: 27121908 DOI: 10.1111/jipb.12482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/20/2016] [Indexed: 05/22/2023]
Abstract
Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are established during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing (AS). However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 34% of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.
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Affiliation(s)
- Arunkumar Srinivasan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Open Analytics, Antwerp, Belgium
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Versailles, France
| | - Fabio Fornara
- University of Milan, Department of Biosciences, Milano 20133, Italy
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vittoria Brambilla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- University of Milan, Department of Biosciences, Milano 20133, Italy
- University of Milan, Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milano, Italy
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22
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Zinsmeister J, Lalanne D, Terrasson E, Chatelain E, Vandecasteele C, Vu BL, Dubois-Laurent C, Geoffriau E, Signor CL, Dalmais M, Gutbrod K, Dörmann P, Gallardo K, Bendahmane A, Buitink J, Leprince O. ABI5 Is a Regulator of Seed Maturation and Longevity in Legumes. THE PLANT CELL 2016; 28:2735-2754. [PMID: 27956585 PMCID: PMC5155344 DOI: 10.1105/tpc.16.00470] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/03/2016] [Accepted: 11/15/2016] [Indexed: 05/18/2023]
Abstract
The preservation of our genetic resources and production of high-quality seeds depends on their ability to remain viable and vigorous during storage. In a quantitative trait locus analysis on seed longevity in Medicago truncatula, we identified the bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5). Characterization of Mt-abi5 insertion mutant seeds revealed that both the acquisition of longevity and dormancy were severely impaired. Using transcriptomes of developing Mt-abi5 seeds, we created a gene coexpression network and revealed ABI5 as a regulator of gene modules with functions related to raffinose family oligosaccharide (RFO) metabolism, late embryogenesis abundant (LEA) proteins, and photosynthesis-associated nuclear genes (PhANGs). Lower RFO contents in Mt-abi5 seeds were linked to the regulation of SEED IMBIBITION PROTEIN1 Proteomic analysis confirmed that a set of LEA polypeptides was reduced in mature Mt-abi5 seeds, whereas the absence of repression of PhANG in mature Mt-abi5 seeds was accompanied by chlorophyll and carotenoid retention. This resulted in a stress response in Mt-abi5 seeds, evident from an increase in α-tocopherol and upregulation of genes related to programmed cell death and protein folding. Characterization of abi5 mutants in a second legume species, pea (Pisum sativum), confirmed a role for ABI5 in the regulation of longevity, seed degreening, and RFO accumulation, identifying ABI5 as a prominent regulator of late seed maturation in legumes.
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Affiliation(s)
- Julia Zinsmeister
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - David Lalanne
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Emmanuel Terrasson
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Emilie Chatelain
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Céline Vandecasteele
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Benoit Ly Vu
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Cécile Dubois-Laurent
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Emmanuel Geoffriau
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | | | - Marion Dalmais
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, 91405 Orsay, France
| | - Katharina Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Karine Gallardo
- Agroécologie, UMR1347, INRA, BP 86510, F-21000 Dijon, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, 91405 Orsay, France
| | - Julia Buitink
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Olivier Leprince
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
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23
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Costa MCD, Farrant JM, Oliver MJ, Ligterink W, Buitink J, Hilhorst HMW. Key genes involved in desiccation tolerance and dormancy across life forms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 251:162-168. [PMID: 27593474 DOI: 10.1016/j.plantsci.2016.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/27/2016] [Accepted: 02/01/2016] [Indexed: 05/25/2023]
Abstract
Desiccation tolerance (DT, the ability of certain organisms to survive severe dehydration) was a key trait in the evolution of life in terrestrial environments. Likely, the development of desiccation-tolerant life forms was accompanied by the acquisition of dormancy or a dormancy-like stage as a second powerful adaptation to cope with variations in the terrestrial environment. These naturally stress tolerant life forms may be a good source of genetic information to generate stress tolerant crops to face a future with predicted higher occurrence of drought. By mining for key genes and mechanisms related to DT and dormancy conserved across different species and life forms, unique candidate key genes may be identified. Here we identify several of these putative key genes, shared among multiple organisms, encoding for proteins involved in protection, growth and energy metabolism. Mutating a selection of these genes in the model plant Arabidopsis thaliana resulted in clear DT-, dormancy- and other seed-associated phenotypes, showing the efficiency and power of our approach and paves the way for the development of drought-stress tolerant crops. Our analysis supports a co-evolution of DT and dormancy by shared mechanisms that favour survival and adaptation to ever-changing environments with strong seasonal fluctuations.
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Affiliation(s)
- Maria Cecília D Costa
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - Melvin J Oliver
- U.S. Department of Agriculture-ARS-MWA-PGRU, 205 Curtis Hall, University of Missouri, Columbia, MO 65211, USA
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Julia Buitink
- Institut National de la Recherch Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Qualité et Santé du Végétal, 49045 Angers, France
| | - Henk M W Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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24
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Kang Y, Li M, Sinharoy S, Verdier J. A Snapshot of Functional Genetic Studies in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1175. [PMID: 27555857 PMCID: PMC4977297 DOI: 10.3389/fpls.2016.01175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Minguye Li
- University of Chinese Academy of SciencesBeijing, China
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Senjuti Sinharoy
- Department of Biotechnology, University of CalcuttaCalcutta, India
| | - Jerome Verdier
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Jerome Verdier
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25
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Moore JP, Farrant JM. Editorial: Current advances and challenges in understanding plant desiccation tolerance. FRONTIERS IN PLANT SCIENCE 2015; 6:768. [PMID: 26483800 PMCID: PMC4586587 DOI: 10.3389/fpls.2015.00768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/07/2015] [Indexed: 05/28/2023]
Affiliation(s)
- John P. Moore
- Department of Viticulture and Oenology, Faculty of AgriSciences, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Jill M. Farrant
- Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
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26
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Costa MCD, Righetti K, Nijveen H, Yazdanpanah F, Ligterink W, Buitink J, Hilhorst HWM. A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds. PLANTA 2015; 242:435-49. [PMID: 25809152 PMCID: PMC4498281 DOI: 10.1007/s00425-015-2283-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/16/2015] [Indexed: 05/19/2023]
Abstract
During re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state. Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT.
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Affiliation(s)
- Maria Cecília D Costa
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands,
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27
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Dekkers BJW, Costa MCD, Maia J, Bentsink L, Ligterink W, Hilhorst HWM. Acquisition and loss of desiccation tolerance in seeds: from experimental model to biological relevance. PLANTA 2015; 241:563-77. [PMID: 25567203 DOI: 10.1007/s00425-014-2240-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/25/2014] [Indexed: 05/20/2023]
Abstract
Besides being an important model to study desiccation tolerance, the induction of desiccation tolerance in germinated seeds may also play an ecological role in seedling establishment. Desiccation tolerance (DT) is the ability of certain organisms to survive extreme water losses without accumulation of lethal damage. This was a key feature in the conquering of dry land and is currently found in all taxa including bacteria, fungi, roundworms and plants. Not surprisingly, studies in various fields have been performed to unravel this intriguing phenomenon. In flowering plants, DT is rare in whole plants (vegetative tissues), yet is common in seeds. In this review, we present our current understanding of the evolution of DT in plants. We focus on the acquisition of DT in seeds and the subsequent loss during and after germination by highlighting and comparing research in two model plants Medicago truncatula and Arabidopsis thaliana. Finally, we discuss the ability of seeds to re-establish DT during post-germination, the possible ecological meaning of this phenomenon, and the hypothesis that DT, in combination with dormancy, optimizes seedling establishment.
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Affiliation(s)
- Bas J W Dekkers
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands,
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Abstract
Anhydrobiosis (Life Without Water) has been known for millennia, but the underlying mechanisms have not been understood until recent decades, and we have achieved only a partial understanding. One of the chief sites of damage from dehydration is membranes, and we and others have provided evidence that this damage may be obviated by the production of certain sugars, particularly trehalose. The sugar stabilizes membranes by preventing fusion and fluidizing the dry bilayers. The mechanism by which this is accomplished has been controversial, and I review that controversy here. In the past decade evidence is accumulating for a role of stress proteins in addition to or as a substitute for trehalose. Genomic studies on anhydrobiotes are yielding rapid progress. Also in the past decade, numerous uses for trehalose in treating human diseases have been proposed, some of which are in clinical testing. I conclude that the mechanisms underlying anhydrobiosis are more complex than we thought 20 years ago, but progress is being made towards elucidating those mechanisms.
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Affiliation(s)
- John H Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95618, USA.
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29
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Crowe JH. Anhydrobiosis: an unsolved problem. PLANT, CELL & ENVIRONMENT 2014; 37:1491-1493. [PMID: 24548118 DOI: 10.1111/pce.12304] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 02/08/2014] [Indexed: 06/03/2023]
Affiliation(s)
- John H Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616
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