1
|
de Freitas Pereira M, Cohen D, Auer L, Aubry N, Bogeat-Triboulot MB, Buré C, Engle NL, Jolivet Y, Kohler A, Novák O, Pavlović I, Priault P, Tschaplinski TJ, Hummel I, Vaultier MN, Veneault-Fourrey C. Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling. Plant J 2023; 116:1784-1803. [PMID: 37715981 DOI: 10.1111/tpj.16465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Tree growth and survival are dependent on their ability to perceive signals, integrate them, and trigger timely and fitted molecular and growth responses. While ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems, little is known about how and to what extent it helps trees cope with environmental changes. We hypothesized that the presence of Laccaria bicolor influences abiotic cue perception by Populus trichocarpa and the ensuing signaling cascade. We submitted ectomycorrhizal or non-ectomycorrhizal P. trichocarpa cuttings to short-term cessation of watering or ozone fumigation to focus on signaling networks before the onset of any physiological damage. Poplar gene expression, metabolite levels, and hormone levels were measured in several organs (roots, leaves, mycorrhizas) and integrated into networks. We discriminated the signal responses modified or maintained by ectomycorrhization. Ectomycorrhizas buffered hormonal changes in response to short-term environmental variations systemically prepared the root system for further fungal colonization and alleviated part of the root abscisic acid (ABA) signaling. The presence of ectomycorrhizas in the roots also modified the leaf multi-omics landscape and ozone responses, most likely through rewiring of the molecular drivers of photosynthesis and the calcium signaling pathway. In conclusion, P. trichocarpa-L. bicolor symbiosis results in a systemic remodeling of the host's signaling networks in response to abiotic changes. In addition, ectomycorrhizal, hormonal, metabolic, and transcriptomic blueprints are maintained in response to abiotic cues, suggesting that ectomycorrhizas are less responsive than non-mycorrhizal roots to abiotic challenges.
Collapse
Affiliation(s)
| | - David Cohen
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Lucas Auer
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
| | - Nathalie Aubry
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | | | - Cyril Buré
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Nancy L Engle
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Yves Jolivet
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Iva Pavlović
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Pierrick Priault
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | - Timothy J Tschaplinski
- Plant Systems Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Irène Hummel
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, F-54000, Nancy, France
| | | | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, Laboratory of Excellence ARBRE, UMR Interactions Arbres/Microorganismes, F-54000, Nancy, France
| |
Collapse
|
2
|
Colombi T, Eitelberg L, Kolb E, Legué V, Bogeat-Triboulot MB. Genotypic differences in systemic root responses to mechanical obstacles. Physiol Plant 2023; 175:e14094. [PMID: 38148185 DOI: 10.1111/ppl.14094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/08/2023] [Indexed: 12/28/2023]
Abstract
As roots grow through the soil to forage for water and nutrients, they encounter mechanical obstacles such as patches of dense soil and stones that locally impede root growth. Here, we investigated hitherto poorly understood systemic responses of roots to localised root impedance. Seedlings of two wheat genotypes were grown in hydroponics and exposed to impenetrable obstacles constraining the vertical growth of the primary or a single seminal root. We deployed high-resolution in vivo imaging to quantify temporal dynamics of root elongation rate, helical root movement, and root growth direction. The two genotypes exhibited distinctly different patterns of systemic responses to localised root impedance, suggesting different strategies to cope with obstacles, namely stress avoidance and stress tolerance. Shallower growth of unconstrained seminal roots and more pronounced helical movement of unconstrained primary and seminal roots upon localised root impedance characterised the avoidance strategy shown by one genotype. Stress tolerance to localised root impedance, as exhibited by the other genotype, was indicated by relatively fast elongation of primary roots and steeper seminal root growth. These different strategies highlight that the effects of mechanical obstacles on spatiotemporal root growth patterns can differ within species, which may have major implications for resource acquisition and whole-plant growth.
Collapse
Affiliation(s)
- Tino Colombi
- Department of Soil and Environment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Leah Eitelberg
- Department of Soil and Environment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Evelyne Kolb
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université Paris Cité, Paris, France
| | - Valérie Legué
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, France
| | | |
Collapse
|
3
|
Quiros M, Bogeat-Triboulot MB, Couturier E, Kolb E. Plant root growth against a mechanical obstacle: the early growth response of a maize root facing an axial resistance is consistent with the Lockhart model. J R Soc Interface 2022; 19:20220266. [PMID: 35919977 PMCID: PMC9346360 DOI: 10.1098/rsif.2022.0266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plant root growth is dramatically reduced in compacted soils, affecting the growth of the whole plant. Through a model experiment coupling force and kinematics measurements, we probed the force-growth relationship of a primary root contacting a stiff resisting obstacle, which mimics the strongest soil impedance variation encountered by a growing root. The growth of maize roots just emerging from a corseting agarose gel and contacting a force sensor (acting as an obstacle) was monitored by time-lapse imaging simultaneously to the force. The evolution of the velocity field along the root was obtained from kinematics analysis of the root texture with a particle image velocimetry derived technique. A triangular fit was introduced to retrieve the elemental elongation rate or strain rate. A parameter-free model based on the Lockhart law quantitatively predicts how the force at the obstacle modifies several features of the growth distribution (length of the growth zone, maximal elemental elongation rate and velocity) during the first 10 min. These results suggest a strong similarity of the early growth responses elicited either by a directional stress (contact) or by an isotropic perturbation (hyperosmotic bath).
Collapse
Affiliation(s)
- Manon Quiros
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | | | - Etienne Couturier
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot CNRS UMR 7057, 10 Rue Alice Domont et Léonie Ducquet, 75205 Paris Cedex 13, France
| | - Evelyne Kolb
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| |
Collapse
|
4
|
Eckert C, Wildhagen H, Paulo MJ, Scalabrin S, Ballauff J, Schnabel SK, Vendramin V, Keurentjes JJB, Bogeat-Triboulot MB, Taylor G, Polle A. Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought. Sci Data 2022; 9:297. [PMID: 35701429 PMCID: PMC9197931 DOI: 10.1038/s41597-022-01417-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis. Measurement(s) | transcriptome | Technology Type(s) | illumina sequencing | Factor Type(s) | treatment | Sample Characteristic - Organism | Populus nigra | Sample Characteristic - Environment | greenhouse experiment |
Collapse
Affiliation(s)
- Christian Eckert
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Henning Wildhagen
- HAWK University of Applied Sciences and Arts, Faculty of Resource Management, Büsgenweg 1a, 37077, Göttingen, Germany.
| | - Maria João Paulo
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Sabine K Schnabel
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Vera Vendramin
- IGA Technology Services, via Jacopo Linussio 51, Udine, Italy
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Gail Taylor
- Department of Plant Sciences, University of California, One Shields Ave, Davis, CA, USA
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| |
Collapse
|
5
|
Fruleux A, Bogeat-Triboulot MB, Collet C, Deveau A, Saint-André L, Santenoise P, Bonal D. Aboveground overyielding in a mixed temperate forest is not explained by belowground processes. Oecologia 2018; 188:1183-1193. [PMID: 30357528 DOI: 10.1007/s00442-018-4278-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
Abstract
The relationship between forest productivity and tree species diversity has been described in detail, but the underlying processes have yet to be identified. One important issue is to understand which processes are at the origin of observed aboveground overyielding in some mixed forests. We used a beech-maple plantation exhibiting aboveground overyielding to test whether belowground processes could explain this pattern. Soil cores were collected to determine fine root (FR) biomass and vertical distribution. Correlograms were used to detect spatial arrangement. Near-infrared reflectance spectroscopy was used to identify the tree species proportion in the FR samples and spatial root segregation. An isotopic approach was used to identify water acquisition patterns. The structure and the composition of the ectomycorrhizal fungal community were determined by high-throughput sequencing of DNA in the soil samples. We found no spatial pattern for FR biomass or for its vertical distribution along the gradients. No vertical root segregation was found, as FR density for both species decreased with depth in a similar way. The two species displayed similar vertical water acquisition profiles as well, mainly absorbing water from shallow soil layers; hence, niche differentiation for water acquisition was not highlighted here. Significant alterations in the fungal community compositions were detected in function of the percentage of maple in the vicinity of beech. Our findings do not support the commonly suggested drivers of aboveground overyielding in species-diverse forests and suggest that competition reduction or between-species facilitation of belowground resource acquisition may not explain the observed aboveground overyielding.
Collapse
Affiliation(s)
- Alexandre Fruleux
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000, Nancy, France.
| | | | - Catherine Collet
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000, Nancy, France
| | - Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280, Champenoux, France
| | | | - Philippe Santenoise
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000, Nancy, France.,INRA, UR BEF, 54280, Champenoux, France
| | - Damien Bonal
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000, Nancy, France
| |
Collapse
|
6
|
Youssef C, Bizet F, Bastien R, Legland D, Bogeat-Triboulot MB, Hummel I. Quantitative dissection of variations in root growth rate: a matter of cell proliferation or of cell expansion? J Exp Bot 2018; 69:5157-5168. [PMID: 30053124 PMCID: PMC6184812 DOI: 10.1093/jxb/ery272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/16/2018] [Indexed: 05/24/2023]
Abstract
Plant organ growth results from cell production and cell expansion. Deciphering the contribution of each of these processes to growth rate is an important issue in developmental biology. Here, we investigated the cellular processes governing root elongation rate, considering two sources of variation: genotype and disturbance by chemicals (NaCl, polyethylene glycol, H2O2, abscisic acid). Exploiting the adventitious rooting capacity of the Populus genus, and using time-lapse imaging under infrared-light, particle image velocimetry, histological analysis, and kinematics, we quantified the cellular processes involved in root growth variation, and analysed the covariation patterns between growth parameters. The rate of cell production by the root apical meristem and the number of dividing cells were estimated in vivo without destructive measurement. We found that the rate of cell division contributed more to the variation in cell production rate than the number of dividing cells. Regardless of the source of variation, the length of the elongation zone was the best proxy for growth rate, summarizing rates of cell production and cell elongation into a single parameter. Our results demonstrate that cell production rate is the main driver of growth rate, whereas elemental elongation rate is a key driver of short-term growth adjustments.
Collapse
Affiliation(s)
- Chvan Youssef
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, Nancy, France
| | - François Bizet
- UMR PIAF, INRA, Université Clermont Auvergne, Aubière, France
| | - Renaud Bastien
- Department of Collective Behaviour, Max Planck Institute for Ornithology, University of Konstanz, Konstanz, Germany
| | - David Legland
- UMR Biopolymers, Interactions and Assemblies, INRA, Nantes, France
| | | | - Irène Hummel
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, Nancy, France
| |
Collapse
|
7
|
Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nat Plants 2018; 4:440-452. [PMID: 29915331 PMCID: PMC6086335 DOI: 10.1038/s41477-018-0172-3] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/08/2018] [Indexed: 05/18/2023]
Abstract
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
Collapse
Affiliation(s)
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Sébastien Faye
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Isabelle Lesur
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- HelixVenture, Mérignac, France
| | | | | | | | | | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Diévart
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | - Marie-Lara Bouffaud
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | | | | | - David Cohen
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Carole Dossat
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | | | - Arnaud Hecker
- IAM, INRA, Université de Lorraine, Champenoux, France
| | - Sylvie Herrmann
- German Centre for Integrative Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Irène Hummel
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric Lasserre
- Université de Perpignan, UMR 5096, Perpignan, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Olivier Rué
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Franck Salin
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
| | - Marçal Soler
- Université de Toulouse, CNRS, UMR 5546, LRSV, Castanet-Tolosan, France
- Laboratori del Suro, University of Girona, Girona, Spain
| | - Mika Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Amandine Velt
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | | | | | | |
Collapse
|
8
|
Wildhagen H, Paul S, Allwright M, Smith HK, Malinowska M, Schnabel SK, Paulo MJ, Cattonaro F, Vendramin V, Scalabrin S, Janz D, Douthe C, Brendel O, Buré C, Cohen D, Hummel I, Le Thiec D, van Eeuwijk F, Keurentjes JJB, Flexas J, Morgante M, Robson P, Bogeat-Triboulot MB, Taylor G, Polle A. Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra. Tree Physiol 2018; 38:320-339. [PMID: 28541580 PMCID: PMC5982782 DOI: 10.1093/treephys/tpx054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/03/2017] [Indexed: 05/03/2023]
Abstract
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential. The three poplar genotypes differed in wood anatomy, lignin content and saccharification potential. Drought resulted in reduced cambial activity, decreased vessel and fiber lumina, and increased the saccharification potential. The saccharification potential was unrelated to lignin content as well as to most wood anatomical traits. RNA sequencing of the developing xylem revealed that 1.5% of the analyzed genes were differentially expressed in response to drought, while 67% differed among the genotypes. Weighted gene correlation network analysis identified modules of co-expressed genes correlated with saccharification potential. These modules were enriched in gene ontology terms related to cell wall polysaccharide biosynthesis and modification and vesicle transport, but not to lignin biosynthesis. Among the most strongly saccharification-correlated genes, those with regulatory functions, especially kinases, were prominent. We further identified transcription factors whose transcript abundances differed among genotypes, and which were co-regulated with genes for biosynthesis and modifications of hemicelluloses and pectin. Overall, our study suggests that the regulation of pectin and hemicellulose metabolism is a promising target for improving wood quality of second generation bioenergy crops. The causal relationship of the identified genes and pathways with saccharification potential needs to be validated in further experiments.
Collapse
Affiliation(s)
- Henning Wildhagen
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
- HAWK University of Applied Sciences and Arts, Faculty of Resource Management, Büsgenweg 1a, 37077 Göttingen, Germany
| | - Shanty Paul
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Mike Allwright
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Hazel K Smith
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Marta Malinowska
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY233EE, UK
| | - Sabine K Schnabel
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Vera Vendramin
- IGA Technology Services, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Simone Scalabrin
- IGA Technology Services, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Dennis Janz
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Cyril Douthe
- Universidad de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Oliver Brendel
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Cyril Buré
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - David Cohen
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Irène Hummel
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Didier Le Thiec
- EEF, INRA, Université de Lorraine, rue d'Amance, 54280 Champenoux, France
| | - Fred van Eeuwijk
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jaume Flexas
- Universidad de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Michele Morgante
- Università Di Udine, Istituto di Genomica Applicata, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Paul Robson
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY233EE, UK
| | | | - Gail Taylor
- Center for Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Andrea Polle
- Forest Botany and Tree Physiology, Georg-August University of Goettingen, Büsgenweg 2, 37077 Göttingen, Germany
- Corresponding author ()
| |
Collapse
|
9
|
Lafon-Placette C, Le Gac AL, Chauveau D, Segura V, Delaunay A, Lesage-Descauses MC, Hummel I, Cohen D, Jesson B, Le Thiec D, Bogeat-Triboulot MB, Brignolas F, Maury S. Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways. J Exp Bot 2018; 69:537-551. [PMID: 29211860 DOI: 10.1093/jxb/erx409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/25/2017] [Indexed: 05/04/2023]
Abstract
The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem. Using microarray chips, differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were identified for each water regime. The rewatering condition was associated with the highest variations of both gene expression and DNA methylation. Changes in methylation were observed particularly in the body of expressed genes and to a lesser extent in transposable elements. Together, DEGs and DMRs were significantly enriched in genes related to phytohormone metabolism or signaling pathways. Altogether, shoot apical meristem responses to changes in water availability involved coordinated variations in DNA methylation, as well as in gene expression, with a specific targeting of genes involved in hormone pathways, a factor that may enable phenotypic plasticity.
Collapse
Affiliation(s)
| | | | | | | | - Alain Delaunay
- LBLGC EA 1207, INRA, Université d'Orléans, USC 1328, France
| | | | - Irène Hummel
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | - David Cohen
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | | | - Didier Le Thiec
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | | | | | - Stéphane Maury
- LBLGC EA 1207, INRA, Université d'Orléans, USC 1328, France
| |
Collapse
|
10
|
|
11
|
Bizet F, Dupuy LX, Bengough AG, Peaucelle A, Hummel I, Bogeat-Triboulot MB. Non-invasive Protocol for Kinematic Monitoring of Root Growth under Infrared Light. Bio Protoc 2017; 7:e2390. [PMID: 34541126 DOI: 10.21769/bioprotoc.2390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/18/2017] [Accepted: 06/08/2017] [Indexed: 11/02/2022] Open
Abstract
Phenotyping the dynamics of root responses to environmental cues is necessary to understand plant acclimation to their environment. Continuous monitoring of root growth is challenging because roots normally grow belowground and are very sensitive to their growth environment. This protocol combines infrared imaging with hydroponic cultivation for kinematic analyses. It allows continuous imaging at fine spatiotemporal resolution and disturbs roots minimally. Examples are provided of how the procedure and materials can be adapted for 3D monitoring and of how environmental stress may be manipulated for experimental purposes.
Collapse
Affiliation(s)
| | | | - Anthony Glyn Bengough
- James Hutton Institute, Dundee, UK.,School of Science and Engineering, University of Dundee, Dundee, UK
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Irène Hummel
- EEF, INRA, Université de Lorraine, Champenoux, France
| | | |
Collapse
|
12
|
Royer M, Cohen D, Aubry N, Vendramin V, Scalabrin S, Cattonaro F, Bogeat-Triboulot MB, Hummel I. The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing. J Exp Bot 2016; 67:5961-5973. [PMID: 27702994 PMCID: PMC5100013 DOI: 10.1093/jxb/erw350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Molecular regulation of growth must include spatial and temporal coupling of cell production and cell expansion. The underlying mechanisms, especially under environmental challenge, remain obscure. Spatial patterns of cell processes make the root apex well suited to deciphering stress signaling pathways, and to investigating both processes. Kinematics and RNA-sequencing were used to analyze the immediate growth response of hydroponically grown Populus nigra cuttings submitted to osmotic stress. About 7400 genes and unannotated transcriptionally active regions were differentially expressed between the division and elongation zones. Following the onset of stress, growth decreased sharply, probably due to mechanical effects, before recovering partially. Stress impaired cell expansion over the apex, progressively shortened the elongation zone, and reduced the cell production rate. Changes in gene expression revealed that growth reduction was mediated by a shift in hormone homeostasis. Osmotic stress rapidly elicited auxin, ethylene, and abscisic acid. When growth restabilized, transcriptome remodeling became complex and zone specific, with the deployment of hormone signaling cascades, transcriptional regulators, and stress-responsive genes. Most transcriptional regulations fit growth reduction, but stress also promoted expression of some growth effectors, including aquaporins and expansins Together, osmotic stress interfered with growth by activating regulatory proteins rather than by repressing the machinery of expansive growth.
Collapse
Affiliation(s)
- Mathilde Royer
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| | - David Cohen
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| | - Nathalie Aubry
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| | | | | | | | | | - Irène Hummel
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| |
Collapse
|
13
|
Bizet F, Bengough AG, Hummel I, Bogeat-Triboulot MB, Dupuy LX. 3D deformation field in growing plant roots reveals both mechanical and biological responses to axial mechanical forces. J Exp Bot 2016; 67:5605-5614. [PMID: 27664958 PMCID: PMC5066484 DOI: 10.1093/jxb/erw320] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Strong regions and physical barriers in soils may slow root elongation, leading to reduced water and nutrient uptake and decreased yield. In this study, the biomechanical responses of roots to axial mechanical forces were assessed by combining 3D live imaging, kinematics and a novel mechanical sensor. This system quantified Young's elastic modulus of intact poplar roots (32MPa), a rapid <0.2 mN touch-elongation sensitivity, and the critical elongation force applied by growing roots that resulted in bending. Kinematic analysis revealed a multiphase bio-mechanical response of elongation rate and curvature in 3D. Measured critical elongation force was accurately predicted from an Euler buckling model, indicating that no biologically mediated accommodation to mechanical forces influenced bending during this short period of time. Force applied by growing roots increased more than 15-fold when buckling was prevented by lateral bracing of the root. The junction between the growing and the mature zones was identified as a zone of mechanical weakness that seemed critical to the bending process. This work identified key limiting factors for root growth and buckling under mechanical constraints. The findings are relevant to crop and soil sciences, and advance our understanding of root growth in heterogeneous structured soils.
Collapse
Affiliation(s)
- François Bizet
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| | - A Glyn Bengough
- James Hutton Institute, Ecological Sciences group, Dundee DD2 5DA, UK School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Irène Hummel
- UMR EEF, INRA, Université de Lorraine, 54280 Champenoux, France
| | | | - Lionel X Dupuy
- James Hutton Institute, Ecological Sciences group, Dundee DD2 5DA, UK
| |
Collapse
|
14
|
Bizet F, Bogeat-Triboulot MB, Montpied P, Christophe A, Ningre N, Cohen D, Hummel I. Phenotypic plasticity toward water regime: response of leaf growth and underlying candidate genes in Populus. Physiol Plant 2015; 154:39-53. [PMID: 25185760 DOI: 10.1111/ppl.12271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/10/2014] [Accepted: 07/23/2014] [Indexed: 06/03/2023]
Abstract
Phenotypic plasticity is considered as an important mechanism for plants to cope with environmental challenges. Leaf growth is one of the first macroscopic processes to be impacted by modification of soil water availability. In this study, we intended to analyze and compare plasticity at different scales. We examined the differential effect of water regime (optimal, moderate water deprivation and recovery) on growth and on the expression of candidate genes in leaves of different growth stages. Candidates were selected to assess components of growth response: abscisic acid signaling, water transport, cell wall modification and stomatal development signaling network. At the tree scale, the four studied poplar hybrids responded similarly to water regime. Meanwhile, leaf growth response was under genotype × environment interaction. Patterns of candidate gene expression enriched our knowledge about their functionality in poplars. For most candidates, transcript levels were strongly structured according to leaf growth performance while response to water regime was clearly dependent on genotype. The use of an index of plasticity revealed that the magnitude of the response was higher for gene expression than for macroscopic traits. In addition, the ranking of poplar genotypes for macroscopic traits well paralleled the one for gene expression.
Collapse
Affiliation(s)
- François Bizet
- INRA, UMR Ecologie et Ecophysiologie Forestières, FR-54280, Champenoux, France; Université de Lorraine, UMR Ecologie et Ecophysiologie Forestières, Faculté des Sciences et Technologies, FR-54506, Vandœuvre-lès-Nancy Cedex, France
| | | | | | | | | | | | | |
Collapse
|
15
|
Bizet F, Bogeat-Triboulot MB, Montpied P, Christophe A, Ningre N, Cohen D, Hummel I. Phenotypic plasticity toward water regime: response of leaf growth and underlying candidate genes in Populus. Physiol Plant 2015; 154:39-53. [PMID: 25185760 DOI: 10.1111/ppl.2015.154.issue-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/10/2014] [Accepted: 07/23/2014] [Indexed: 05/27/2023]
Abstract
Phenotypic plasticity is considered as an important mechanism for plants to cope with environmental challenges. Leaf growth is one of the first macroscopic processes to be impacted by modification of soil water availability. In this study, we intended to analyze and compare plasticity at different scales. We examined the differential effect of water regime (optimal, moderate water deprivation and recovery) on growth and on the expression of candidate genes in leaves of different growth stages. Candidates were selected to assess components of growth response: abscisic acid signaling, water transport, cell wall modification and stomatal development signaling network. At the tree scale, the four studied poplar hybrids responded similarly to water regime. Meanwhile, leaf growth response was under genotype × environment interaction. Patterns of candidate gene expression enriched our knowledge about their functionality in poplars. For most candidates, transcript levels were strongly structured according to leaf growth performance while response to water regime was clearly dependent on genotype. The use of an index of plasticity revealed that the magnitude of the response was higher for gene expression than for macroscopic traits. In addition, the ranking of poplar genotypes for macroscopic traits well paralleled the one for gene expression.
Collapse
Affiliation(s)
- François Bizet
- INRA, UMR Ecologie et Ecophysiologie Forestières, FR-54280, Champenoux, France; Université de Lorraine, UMR Ecologie et Ecophysiologie Forestières, Faculté des Sciences et Technologies, FR-54506, Vandœuvre-lès-Nancy Cedex, France
| | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
Understanding how cell division and cell elongation influence organ growth and development is a long-standing issue in plant biology. In plant roots, most of the cell divisions occur in a short and specialized region, the root apical meristem (RAM). Although RAM activity has been suggested to be of high importance to understand how roots grow and how the cell cycle is regulated, few experimental and numeric data are currently available. The characterization of the RAM is difficult and essentially based upon cell length measurements through destructive and time-consuming microscopy approaches. Here, a new non-invasive method is described that couples infrared light imaging and kinematic analyses and that allows in vivo measurements of the RAM length. This study provides a detailed description of the RAM activity, especially in terms of cell flux and cell division rate. We focused on roots of hydroponic grown poplars and confirmed our method on maize roots. How the RAM affects root growth rate is studied by taking advantage of the high inter-individual variability of poplar root growth. An osmotic stress was applied and did not significantly affect the RAM length, highlighting its homeostasis in short to middle-term responses. The methodology described here simplifies a lot experimental procedures, allows an increase in the number of individuals that can be taken into account in experiments, and means new experiments can be formulated that allow temporal monitoring of the RAM length.
Collapse
Affiliation(s)
- François Bizet
- INRA, UMR Ecologie et Ecophysiologie Forestière, F-25420 Champenoux, France Université de Lorraine, UMR Ecologie et Ecophysiologie Forestière, BP 239, F-54506 Vandoeuvre, France
| | - Irène Hummel
- INRA, UMR Ecologie et Ecophysiologie Forestière, F-25420 Champenoux, France Université de Lorraine, UMR Ecologie et Ecophysiologie Forestière, BP 239, F-54506 Vandoeuvre, France
| | - Marie-Béatrice Bogeat-Triboulot
- INRA, UMR Ecologie et Ecophysiologie Forestière, F-25420 Champenoux, France Université de Lorraine, UMR Ecologie et Ecophysiologie Forestière, BP 239, F-54506 Vandoeuvre, France
| |
Collapse
|
17
|
Cohen D, Bogeat-Triboulot MB, Vialet-Chabrand S, Merret R, Courty PE, Moretti S, Bizet F, Guilliot A, Hummel I. Developmental and environmental regulation of Aquaporin gene expression across Populus species: divergence or redundancy? PLoS One 2013; 8:e55506. [PMID: 23393587 PMCID: PMC3564762 DOI: 10.1371/journal.pone.0055506] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 12/24/2012] [Indexed: 11/29/2022] Open
Abstract
Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy could be suspected.
Collapse
Affiliation(s)
- David Cohen
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Marie-Béatrice Bogeat-Triboulot
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
- * E-mail:
| | - Silvère Vialet-Chabrand
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Rémy Merret
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Pierre-Emmanuel Courty
- Zürich-Basel Plant Science Center, Botanical Institute, University of Basel, Basel, Switzerland
| | - Sébastien Moretti
- Vital-IT, SIB Swiss Institute of Bioinformatics, Quartier Sorge, bâtiment Génopode, Lausanne, Switzerland
- Department of Ecology and Evolution, bâtiment Biophore, Lausanne University, Lausanne, Switzerland
| | - François Bizet
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Agnès Guilliot
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Irène Hummel
- INRA, UMR1137 Ecologie et Ecophysiologie Forestières, Champenoux, France
- Université de Lorraine, UMR1137 Ecologie et Ecophysiologie Forestières, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| |
Collapse
|
18
|
Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I. Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 2010; 11:630. [PMID: 21073700 PMCID: PMC3091765 DOI: 10.1186/1471-2164-11-630] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/12/2010] [Indexed: 12/18/2022] Open
Abstract
Background Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species. Results Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought. Conclusions In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.
Collapse
Affiliation(s)
- David Cohen
- INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Merret R, Moulia B, Hummel I, Cohen D, Dreyer E, Bogeat-Triboulot MB. Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism. BMC Biol 2010; 8:18. [PMID: 20202192 PMCID: PMC2845557 DOI: 10.1186/1741-7007-8-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 03/04/2010] [Indexed: 01/09/2023] Open
Abstract
Background Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring during development requires a specific framework that properly quantifies the rate of change of a property in a moving and expanding element, such as a cell or an organ segment. Results We show how the rate of change in gene expression can be quantified by combining kinematics and real-time polymerase chain reaction data in a mechanistic model which considers any organ as a continuum. This framework was applied in order to assess the developmental regulation of the two reference genes Actin11 and Elongation Factor 1-β in the apex of poplar root. The growth field was determined by time-lapse photography and transcript density was obtained at high spatial resolution. The net accumulation rates of the transcripts of the two genes were found to display highly contrasted developmental profiles. Actin11 showed pulses of up and down regulation in the accelerating and decelerating parts of the growth zone while the dynamic of EF1β were much slower. This framework provides key information about gene regulation in a developing organ, such as the location, the duration and the intensity of gene induction/repression. Conclusions We demonstrated that gene expression patterns can be monitored using the continuity equation without using mutants or reporter constructions. Given the rise of imaging technologies, this framework in our view opens a new way to dissect the molecular basis of growth regulation, even in non-model species or complex structures.
Collapse
Affiliation(s)
- Rémy Merret
- INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France
| | | | | | | | | | | |
Collapse
|
20
|
Plomion C, Lalanne C, Claverol S, Meddour H, Kohler A, Bogeat-Triboulot MB, Barre A, Le Provost G, Dumazet H, Jacob D, Bastien C, Dreyer E, de Daruvar A, Guehl JM, Schmitter JM, Martin F, Bonneu M. Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins. Proteomics 2007; 6:6509-27. [PMID: 17163438 DOI: 10.1002/pmic.200600362] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Poplar is the first forest tree genome to be decoded. As an initial step to the comprehensive analysis of poplar proteome, we described reference 2-D-maps for eight tissues/organs of the plant, and the functional characterization of some proteins. A total of 398 proteins were excised from the gels. About 91.2% were identified by nanospray LC-MS/MS, based on comparison with 260,000 Populus sp. ESTs. In comparison, reliable PMFs were obtained for only 51% of the spots by MALDI-TOF-MS, from which 43% (83 spots) positively matched gene models of the Populus trichocarpa genome sequence. Among these 83 spots, 58% matched with the same proteins as identified by LC-MS/MS, 21.7% with unknown function proteins and 19.3% with completely different functions. In the second phase, we studied the effect of drought stress on poplar root and leaf proteomes. The function of up- and down-regulated proteins is discussed with respect to the physiological response of the plants and compared with transcriptomic data. Some important clues regarding the way poplar copes with water deficit were revealed.
Collapse
Affiliation(s)
- Christophe Plomion
- UMR Biodiversité Gènes Communautés, INRA, Equipe de génétique, Cestas, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Bogeat-Triboulot MB, Brosché M, Renaut J, Jouve L, Le Thiec D, Fayyaz P, Vinocur B, Witters E, Laukens K, Teichmann T, Altman A, Hausman JF, Polle A, Kangasjärvi J, Dreyer E. Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. Plant Physiol 2007; 143:876-92. [PMID: 17158588 PMCID: PMC1803728 DOI: 10.1104/pp.106.088708] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 11/21/2006] [Indexed: 05/06/2023]
Abstract
The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated.
Collapse
Affiliation(s)
- Marie-Béatrice Bogeat-Triboulot
- Institut National de la Recherche Agronomique Nancy, Unité Mixte de Recherche 1137 Institut National de la Recherche Agronomique-Université Henri Poincaré Ecologie et Ecophysiologie Forestières, F-54280 Champenoux, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Brosché M, Vinocur B, Alatalo ER, Lamminmäki A, Teichmann T, Ottow EA, Djilianov D, Afif D, Bogeat-Triboulot MB, Altman A, Polle A, Dreyer E, Rudd S, Paulin L, Auvinen P, Kangasjärvi J. Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol 2005; 6:R101. [PMID: 16356264 PMCID: PMC1414072 DOI: 10.1186/gb-2005-6-12-r101] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 07/22/2005] [Accepted: 11/02/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline semi-arid areas. To identify genes involved in abiotic stress responses under natural conditions we constructed several normalized and subtracted cDNA libraries from control, stress-exposed and desert-grown P. euphratica trees. In addition, we identified several metabolites in desert-grown P. euphratica trees. RESULTS About 14,000 expressed sequence tag (EST) sequences were obtained with a good representation of genes putatively involved in resistance and tolerance to salt and other abiotic stresses. A P. euphratica DNA microarray with a uni-gene set of ESTs representing approximately 6,340 different genes was constructed. The microarray was used to study gene expression in adult P. euphratica trees growing in the desert canyon of Ein Avdat in Israel. In parallel, 22 selected metabolites were profiled in the same trees. CONCLUSION Of the obtained ESTs, 98% were found in the sequenced P. trichocarpa genome and 74% in other Populus EST collections. This implies that the P. euphratica genome does not contain different genes per se, but that regulation of gene expression might be different and that P. euphratica expresses a different set of genes that contribute to adaptation to saline growth conditions. Also, all of the five measured amino acids show increased levels in trees growing in the more saline soil.
Collapse
Affiliation(s)
- Mikael Brosché
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Viikinkaari 1, FIN-00014 Helsinki, Finland
| | - Basia Vinocur
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Herzl Street, Rehovot 76100, Israel
| | - Edward R Alatalo
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland
| | - Airi Lamminmäki
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Viikinkaari 1, FIN-00014 Helsinki, Finland
| | - Thomas Teichmann
- Institut für Forstbotanik, Georg-August-Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Eric A Ottow
- Institut für Forstbotanik, Georg-August-Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | | | - Dany Afif
- UMR INRA-UHP Ecologie et Ecophysiologie Forestières, Faculté des Sciences, F-54506 Vandoeuvre, France
| | - Marie-Béatrice Bogeat-Triboulot
- UMR INRA-UHP Ecologie et Ecophysiologie Forestières, IFR 110 Génomique, Ecophysiologie et Ecologie Fonctionnelle, INRA Nancy, Route d'Amance, F-54280 Champenoux, France
| | - Arie Altman
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Herzl Street, Rehovot 76100, Israel
| | - Andrea Polle
- Institut für Forstbotanik, Georg-August-Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Erwin Dreyer
- UMR INRA-UHP Ecologie et Ecophysiologie Forestières, IFR 110 Génomique, Ecophysiologie et Ecologie Fonctionnelle, INRA Nancy, Route d'Amance, F-54280 Champenoux, France
| | - Stephen Rudd
- Turku Centre for Biotechnology, BioCity, Tykistökatu 6, FIN-20521 Turku, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland
| | - Jaakko Kangasjärvi
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Viikinkaari 1, FIN-00014 Helsinki, Finland
| |
Collapse
|
23
|
Hukin D, Cochard H, Dreyer E, Le Thiec D, Bogeat-Triboulot MB. Cavitation vulnerability in roots and shoots: does Populus euphratica Oliv., a poplar from arid areas of Central Asia, differ from other poplar species? J Exp Bot 2005; 56:2003-10. [PMID: 15967780 DOI: 10.1093/jxb/eri198] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Populus euphratica is a poplar species growing in arid regions of Central Asia, where its distribution remains nevertheless restricted to river-banks or to areas with an access to deep water tables. To test whether the hydraulic architecture of this species differs from that of other poplars with respect to this ecological distribution, the vulnerability to cavitation of P. euphratica was compared with that of P. alba and of P. trichocarpa x koreana. The occurrence of a potential hydraulic segmentation through cavitation was also investigated by assessing the vulnerability of roots, stems, and leaf mid-rib veins. Cryo-scanning electron microscopy (cryo-SEM) was used to assess the level of embolism in fine roots and leaf mid-ribs and a low pressure flowmeter (LPFM) was used for stems and main roots. The cryo-SEM technique was validated against LPFM measurements on paired samples. In P. alba and P. trichocarpa x koreana, leaf mid-ribs were more vulnerable to cavitation than stems and roots. In P. euphratica, leaf mid-ribs and stems were equally vulnerable and, contrary to what has been observed in other species, roots were significantly less vulnerable than shoots. P. euphratica was by far the most vulnerable. The water potential inducing 50% loss of conductivity in stems was close to -0.7 MPa, against approximately -1.45 MPa for the two others species. Such a large vulnerability was confirmed by recording losses of conductivity during a gradual drought. Moreover, significant stem embolism was recorded before stomatal closure, indicating the lack of an efficient safety margin for hydraulic functions in this species. Embolism was not reversed by rewatering. These observations are discussed with respect to the ecology of P. euphratica.
Collapse
Affiliation(s)
- D Hukin
- UMR INRA-UHP Ecologie-Ecophysiologie Forestières, INRA Nancy, F-54280 Champenoux, France
| | | | | | | | | |
Collapse
|
24
|
Abstract
The effects of temperature on root and shoot hydraulic conductances (g(shoot) and g(root)) were investigated for Quercus robur L. saplings. In a first experiment, conductances were measured with a High Pressure Flow Meter on excised shoots and detopped root systems. The g(root) and g(shoot) increased considerably with temperature from 0-50 degrees C. Between 15 degrees C and 35 degrees C, g(shoot) and g(root) varied with water viscosity. In a second experiment, the impact of temperature-induced changes in g(root) on sapling transpiration (E) and leaf water potential (psileaf) was assessed. Intact plants were placed in a growth cabinet with constant air and variable soil temperatures. E increased linearly with soil temperature but psileaf remained constant. As a consequence, a linear relationship was found between E and g(plant). The results illustrate the significance of g(plant) for the stomatal control of transpiration and the significance of temperature for tree water transport.
Collapse
Affiliation(s)
- H Cochard
- UA-PIAF, INRA, Clermont-Ferrand, France.
| | | | | | | |
Collapse
|
25
|
Bogeat-Triboulot MB, Lévy G. Contribution of different solutes to the cell osmotic pressure in tap and lateral roots of maritime pine seedlings: effects of a potassium deficiency and of an all-macronutrient deficiency. ACTA ACUST UNITED AC 1998. [DOI: 10.1051/forest:19980304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|