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Takawira LT, Hadj Bachir I, Ployet R, Tulloch J, San Clemente H, Christie N, Ladouce N, Dupas A, Rai A, Grima-Pettenati J, Myburg AA, Mizrachi E, Mounet F, Hussey SG. Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML. Plant Mol Biol 2023; 113:33-57. [PMID: 37661236 DOI: 10.1007/s11103-023-01376-y] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.
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Affiliation(s)
- Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Ines Hadj Bachir
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jade Tulloch
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Helene San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Annabelle Dupas
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Avanish Rai
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France.
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
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Cao PB, Ployet R, Nguyen C, Dupas A, Ladouce N, Martinez Y, Grima-Pettenati J, Marque C, Mounet F, Teulières C. Wood Architecture and Composition Are Deeply Remodeled in Frost Sensitive Eucalyptus Overexpressing CBF/DREB1 Transcription Factors. Int J Mol Sci 2020; 21:ijms21083019. [PMID: 32344718 PMCID: PMC7215815 DOI: 10.3390/ijms21083019] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 02/03/2023] Open
Abstract
Eucalypts are the most planted trees worldwide, but most of them are frost sensitive. Overexpressing transcription factors for CRT-repeat binding factors (CBFs) in transgenic Eucalyptus confer cold resistance both in leaves and stems. While wood plays crucial roles in trees and is affected by environmental cues, its potential role in adaptation to cold stress has been neglected. Here, we addressed this question by investigating the changes occurring in wood in response to the overexpression of two CBFs, taking advantage of available transgenic Eucalyptus lines. We performed histological, biochemical, and transcriptomic analyses on xylem samples. CBF ectopic expression led to a reduction of both primary and secondary growth, and triggered changes in xylem architecture with smaller and more frequent vessels and fibers exhibiting reduced lumens. In addition, lignin content and syringyl/guaiacyl (S/G) ratio increased. Consistently, many genes of the phenylpropanoid and lignin branch pathway were upregulated. Most of the features of xylem remodeling induced by CBF overexpression are reminiscent of those observed after long exposure of Eucalyptus trees to chilling temperatures. Altogether, these results suggest that CBF plays a central role in the cross-talk between response to cold and wood formation and that the remodeling of wood is part of the adaptive strategies to face cold stress.
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Affiliation(s)
- Phi Bang Cao
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
- Department of Natural Sciences, Hung Vuong University, Nong Trang Ward, Viet Tri City, Phu Tho Province 29000, Vietnam
| | - Raphaël Ployet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Chien Nguyen
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
- Biotechnology and crop protection Department; Northern Mountainous Agriculture and Forestry Science Institute, Phu Tho 29000, Vietnam
| | - Annabelle Dupas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
| | - Yves Martinez
- CMEAB, IFR40 Pôle de Biotechnologie Végétale, 31320 Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
| | - Christiane Marque
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
| | - Chantal Teulières
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 31320 Castanet-Tolosan, France; (P.B.C.); (R.P.)
- Correspondence:
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Ployet R, Soler M, Carocha V, Ladouce N, Alves A, Rodrigues JC, Harvengt L, Marque C, Teulières C, Grima-Pettenati J, Mounet F. Long cold exposure induces transcriptional and biochemical remodelling of xylem secondary cell wall in Eucalyptus. Tree Physiol 2018. [PMID: 28633295 DOI: 10.1093/treephys/tpx062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Although eucalypts are the most planted hardwood trees worldwide, the majority of them are frost sensitive. The recent creation of frost-tolerant hybrids such as Eucalyptus gundal plants (E. gunnii × E. dalrympleana hybrids), now enables the development of industrial plantations in northern countries. Our objective was to evaluate the impact of cold on the wood structure and composition of these hybrids, and on the biosynthetic and regulatory processes controlling their secondary cell-wall (SCW) formation. We used an integrated approach combining histology, biochemical characterization and transcriptomic profiling as well as gene co-expression analyses to investigate xylem tissues from Eucalyptus hybrids exposed to cold conditions. Chilling temperatures triggered the deposition of thicker and more lignified xylem cell walls as well as regulation at the transcriptional level of SCW genes. Most genes involved in lignin biosynthesis, except those specifically dedicated to syringyl unit biosynthesis, were up-regulated. The construction of a co-expression network enabled the identification of both known and potential new SCW transcription factors, induced by cold stress. These regulators at the crossroads between cold signalling and SCW formation are promising candidates for functional studies since they may contribute to the tolerance of E. gunnii × E. dalrympleana hybrids to cold.
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Affiliation(s)
- Raphael Ployet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Marçal Soler
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Victor Carocha
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
- Instituto de Tecnologia de Química Biológica (ITQB), Biotecnologia de Células Vegetais, Av. da Republica, 2781-157 Oeiras, Portugal
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Ana Alves
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - José-Carlos Rodrigues
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Luc Harvengt
- FCBA, Biotechnology and Advanced Silviculture Department, Genetics and Biotechnology Team, F-33610 Cestas, France
| | - Christiane Marque
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Chantal Teulières
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
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Nguyen HC, Cao PB, San Clemente H, Ployet R, Mounet F, Ladouce N, Harvengt L, Marque C, Teulieres C. Special trends in CBF and DREB2 groups in Eucalyptus gunnii vs Eucalyptus grandis suggest that CBF are master players in the trade-off between growth and stress resistance. Physiol Plant 2017; 159:445-467. [PMID: 27861954 DOI: 10.1111/ppl.12529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
Annotation of the Eucalyptus grandis genome showed a large amplification of the dehydration-responsive element binding 1/C-repeat binding factor (DREB1/CBF) group without recent DREB2 gene duplication compared with other plant species. The present annotation of the CBF and DREB2 genes from a draft of the Eucalyptus gunnii genome sequence reveals at least one additional CBF copy in the E. gunnii genome compared with E. grandis, suggesting that this group is still evolving, unlike the DREB2 group. This study aims to investigate the redundancy/neo- or sub-functionalization of the duplicates and the relative involvement of the two groups in abiotic stress responses in both E. grandis and E. gunnii (lower growth but higher cold resistance). A comprehensive transcriptional analysis using high-throughput quantitative real-time polymerase chain reaction (qRT-PCR) was performed on leaves, stems and roots from the two Eucalyptus species after cold, heat or drought treatment. A large CBF cluster accounted for most of the cold response in all the organs, whereas heat and drought responses mainly involved a small CBF cluster and the DREB2 genes. In addition, CBF putative target genes, known to be involved in plant tolerance and development, were found to be cold-regulated. The higher transcript amounts of both the CBF and target genes in the cold tolerant E. gunnii contrasted with the higher CBF induction rates in the fast growing E. grandis. Altogether, the present results, in agreement with previous data about Eucalyptus transgenic lines over-expressing CBF, suggest that these factors, which promote both stress protection and growth limitation, participate in the trade-off between growth and resistance in this woody species.
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Affiliation(s)
- Hong C Nguyen
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Phi B Cao
- Hung Vuong University, Nong Trang Ward, Viettri City, Vietnam
| | - Hélène San Clemente
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Raphaël Ployet
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Fabien Mounet
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Nathalie Ladouce
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Luc Harvengt
- FCBA Biotechnology and Advanced Silviculture Dept, Genetics & Biotechnology Team, Cestas, France
| | - Christiane Marque
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
| | - Chantal Teulieres
- Université de Toulouse, UPS, UMR 5546, Plant Research Laboratory (LRSV), Castanet-Tolosan, France
- CNRS, Castanet-Tolosan, France
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Plasencia A, Soler M, Dupas A, Ladouce N, Silva-Martins G, Martinez Y, Lapierre C, Franche C, Truchet I, Grima-Pettenati J. Eucalyptus hairy roots, a fast, efficient and versatile tool to explore function and expression of genes involved in wood formation. Plant Biotechnol J 2016; 14:1381-93. [PMID: 26579999 DOI: 10.1111/pbi.12502] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/02/2015] [Accepted: 10/17/2015] [Indexed: 05/26/2023]
Abstract
Eucalyptus are of tremendous economic importance being the most planted hardwoods worldwide for pulp and paper, timber and bioenergy. The recent release of the Eucalyptus grandis genome sequence pointed out many new candidate genes potentially involved in secondary growth, wood formation or lineage-specific biosynthetic pathways. Their functional characterization is, however, hindered by the tedious, time-consuming and inefficient transformation systems available hitherto for eucalypts. To overcome this limitation, we developed a fast, reliable and efficient protocol to obtain and easily detect co-transformed E. grandis hairy roots using fluorescent markers, with an average efficiency of 62%. We set up conditions both to cultivate excised roots in vitro and to harden composite plants and verified that hairy root morphology and vascular system anatomy were similar to wild-type ones. We further demonstrated that co-transformed hairy roots are suitable for medium-throughput functional studies enabling, for instance, protein subcellular localization, gene expression patterns through RT-qPCR and promoter expression, as well as the modulation of endogenous gene expression. Down-regulation of the Eucalyptus cinnamoyl-CoA reductase1 (EgCCR1) gene, encoding a key enzyme in lignin biosynthesis, led to transgenic roots with reduced lignin levels and thinner cell walls. This gene was used as a proof of concept to demonstrate that the function of genes involved in secondary cell wall biosynthesis and wood formation can be elucidated in transgenic hairy roots using histochemical, transcriptomic and biochemical approaches. The method described here is timely because it will accelerate gene mining of the genome for both basic research and industry purposes.
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Affiliation(s)
- Anna Plasencia
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Marçal Soler
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Annabelle Dupas
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Nathalie Ladouce
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Guilherme Silva-Martins
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Yves Martinez
- FRAIB, CNRS, Cell Imaging Plateform, Castanet Tolosan, France
| | - Catherine Lapierre
- INRA/AgroParisTech, UMR1318, Saclay Plant Science, Jean-Pierre Bourgin Institute (IJPB), Versailles, France
| | | | - Isabelle Truchet
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
| | - Jacqueline Grima-Pettenati
- UMR5546, Toulouse III Paul Sabatier University-CNRS, Plant Research Laboratory (LRSV), Castanet Tolosan, France
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Soler M, Plasencia A, Lepikson-Neto J, Camargo ELO, Dupas A, Ladouce N, Pesquet E, Mounet F, Larbat R, Grima-Pettenati J. The Woody-Preferential Gene EgMYB88 Regulates the Biosynthesis of Phenylpropanoid-Derived Compounds in Wood. Front Plant Sci 2016; 7:1422. [PMID: 27713753 PMCID: PMC5032791 DOI: 10.3389/fpls.2016.01422] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/06/2016] [Indexed: 05/19/2023]
Abstract
Comparative phylogenetic analyses of the R2R3-MYB transcription factor family revealed that five subgroups were preferentially found in woody species and were totally absent from Brassicaceae and monocots (Soler et al., 2015). Here, we analyzed one of these subgroups (WPS-I) for which no gene had been yet characterized. Most Eucalyptus members of WPS-I are preferentially expressed in the vascular cambium, the secondary meristem responsible for tree radial growth. We focused on EgMYB88, which is the most specifically and highly expressed in vascular tissues, and showed that it behaves as a transcriptional activator in yeast. Then, we functionally characterized EgMYB88 in both transgenic Arabidopsis and poplar plants overexpressing either the native or the dominant repression form (fused to the Ethylene-responsive element binding factor-associated Amphiphilic Repression motif, EAR). The transgenic Arabidopsis lines had no phenotype whereas the poplar lines overexpressing EgMYB88 exhibited a substantial increase in the levels of the flavonoid catechin and of some salicinoid phenolic glycosides (salicortin, salireposide, and tremulacin), in agreement with the increase of the transcript levels of landmark biosynthetic genes. A change in the lignin structure (increase in the syringyl vs. guaiacyl, S/G ratio) was also observed. Poplar lines overexpressing the EgMYB88 dominant repression form did not show a strict opposite phenotype. The level of catechin was reduced, but the levels of the salicinoid phenolic glycosides and the S/G ratio remained unchanged. In addition, they showed a reduction in soluble oligolignols containing sinapyl p-hydroxybenzoate accompanied by a mild reduction of the insoluble lignin content. Altogether, these results suggest that EgMYB88, and more largely members of the WPS-I group, could control in cambium and in the first layers of differentiating xylem the biosynthesis of some phenylpropanoid-derived secondary metabolites including lignin.
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Affiliation(s)
- Marçal Soler
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Anna Plasencia
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Jorge Lepikson-Neto
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Eduardo L. O. Camargo
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Annabelle Dupas
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | | | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
| | - Romain Larbat
- “Agronomie et Environnement” Nancy-Colmar, Institut National de la Recherche Agronomique, Université de Lorraine UMR1121Vandœuvre-lès-Nancy, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Centre National de la Recherche Scientifique, Université de Toulouse III, Paul SabatierToulouse, France
- *Correspondence: Jacqueline Grima-Pettenati
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Vergnes S, Ladouce N, Fournier S, Ferhout H, Attia F, Dumas B. Foliar treatments with Gaultheria procumbens essential oil induce defense responses and resistance against a fungal pathogen in Arabidopsis. Front Plant Sci 2014; 5:477. [PMID: 25295045 PMCID: PMC4172006 DOI: 10.3389/fpls.2014.00477] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/29/2014] [Indexed: 05/03/2023]
Abstract
Essential oil from Gaultheria procumbens is mainly composed of methylsalicylate (MeSA) (>96%), a compound which can be metabolized in plant tissues to salicylic acid, a phytohormone inducing plant immunity against microbial pathogens. The potential use of G. procumbens essential oil as a biocontrol agent was evaluated on the model plant Arabidopsis thaliana. Expression of a selection of defense genes was detected 1, 6, and 24 h after essential oil treatment (0.1 ml/L) using a high-throughput qPCR-based microfluidic technology. Control treatments included methyl jasmonate and a commercialized salicylic acid (SA) analog, benzo(1,2,3)-thiadiazole-7carbothiolic acid (BTH). Strong induction of defense markers known to be regulated by the SA pathway was observed after the treatment with G. procumbens essential oil. Treatment induced the accumulation of total SA in the wild-type Arabidopsis line Col-0 and analysis of the Arabidopsis line sid2, mutated in a SA biosynthetic gene, revealed that approximately 30% of MeSA sprayed on the leaves penetrated inside plant tissues and was demethylated by endogenous esterases. Induction of plant resistance by G. procumbens essential oil was tested following inoculation with a GFP-expressing strain of the Arabidopsis fungal pathogen Colletotrichum higginsianum. Fluorescence measurement of infected tissues revealed that treatments led to a strong reduction (60%) of pathogen development and that the efficacy of the G. procumbens essential oil was similar to the commercial product BION(®). Together, these results show that the G. procubens essential oil is a natural source of MeSA which can be formulated to develop new biocontrol products.
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Affiliation(s)
- Sophie Vergnes
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
| | - Nathalie Ladouce
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
| | - Sylvie Fournier
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
| | | | - Faouzi Attia
- Equipe Recherches Agronomiques, AgronutritionCarbonne, France
- LabCom C2R-BIONUTToulouse, France
| | - Bernard Dumas
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences VégétalesCastanet-Tolosan, France
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Larroque M, Belmas E, Martinez T, Vergnes S, Ladouce N, Lafitte C, Gaulin E, Dumas B. Pathogen-associated molecular pattern-triggered immunity and resistance to the root pathogen Phytophthora parasitica in Arabidopsis. J Exp Bot 2013; 64:3615-25. [PMID: 23851194 PMCID: PMC3745725 DOI: 10.1093/jxb/ert195] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 05/20/2023]
Abstract
The cellulose binding elicitor lectin (CBEL) of the genus Phytophthora induces necrosis and immune responses in several plant species, including Arabidopsis thaliana. However, the role of CBEL-induced responses in the outcome of the interaction is still unclear. This study shows that some of CBEL-induced defence responses, but not necrosis, required the receptor-like kinase BAK1, a general regulator of basal immunity in Arabidopsis, and the production of a reactive oxygen burst mediated by respiratory burst oxidases homologues (RBOH). Screening of a core collection of 48 Arabidopsis ecotypes using CBEL uncovered a large variability in CBEL-induced necrotic responses. Analysis of non-responsive CBEL lines Ws-4, Oy-0, and Bla-1 revealed that Ws-4 and Oy-0 were also impaired in the production of the oxidative burst and expression of defence genes, whereas Bla-1 was partially affected in these responses. Infection tests using two Phytophthora parasitica strains, Pp310 and Ppn0, virulent and avirulent, respectively, on the Col-0 line showed that BAK1 and RBOH mutants were susceptible to Ppn0, suggesting that some immune responses controlled by these genes, but not CBEL-induced cell death, are required for Phytophthora parasitica resistance. However, Ws-4, Oy-0, and Bla-1 lines were not affected in Ppn0 resistance, showing that natural variability in CBEL responsiveness is not correlated to Phytophthora susceptibility. Overall, the results uncover a BAK1- and RBOH-dependent CBEL-triggered immunity essential for Phytophthora resistance and suggest that natural quantitative variation of basal immunity triggered by conserved general elicitors such as CBEL does not correlate to Phytophthora susceptibility.
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Affiliation(s)
- Mathieu Larroque
- Université de Toulouse, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
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Cassan-Wang H, Soler M, Yu H, Camargo ELO, Carocha V, Ladouce N, Savelli B, Paiva JAP, Leplé JC, Grima-Pettenati J. Reference genes for high-throughput quantitative reverse transcription-PCR analysis of gene expression in organs and tissues of Eucalyptus grown in various environmental conditions. Plant Cell Physiol 2012; 53:2101-16. [PMID: 23161857 DOI: 10.1093/pcp/pcs152] [Citation(s) in RCA: 31] [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] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Interest in the genomics of Eucalyptus has skyrocketed thanks to the recent sequencing of the genome of Eucalyptus grandis and to a growing number of large-scale transcriptomic studies. Quantitative reverse transcription-PCR (RT-PCR) is the method of choice for gene expression analysis and can now also be used as a high-throughput method. The selection of appropriate internal controls is becoming of utmost importance to ensure accurate expression results in Eucalyptus. To this end, we selected 21 candidate reference genes and used high-throughput microfluidic dynamic arrays to assess their expression among a large panel of developmental and environmental conditions with a special focus on wood-forming tissues. We analyzed the expression stability of these genes by using three distinct statistical algorithms (geNorm, NormFinder and ΔCt), and used principal component analysis to compare methods and rankings. We showed that the most stable genes identified depended not only on the panel of biological samples considered but also on the statistical method used. We then developed a comprehensive integration of the rankings generated by the three methods and identified the optimal reference genes for 17 distinct experimental sets covering 13 organs and tissues, as well as various developmental and environmental conditions. The expression patterns of Eucalyptus master genes EgMYB1 and EgMYB2 experimentally validated our selection. Our findings provide an important resource for the selection of appropriate reference genes for accurate and reliable normalization of gene expression data in the organs and tissues of Eucalyptus trees grown in a range of conditions including abiotic stresses.
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Affiliation(s)
- Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse III, UPS, CNRS, BP 42617, Auzeville, 31326 Castanet Tolosan, France.
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Wang H, Soler M, Yu H, Camargo ELO, Clemente HS, Savelli B, Ladouce N, Paiva J, Grima-Pettenati J. Master regulators of wood formation in Eucalyptus. BMC Proc 2011. [PMCID: PMC3239954 DOI: 10.1186/1753-6561-5-s7-p110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Legay S, Sivadon P, Blervacq AS, Pavy N, Baghdady A, Tremblay L, Levasseur C, Ladouce N, Lapierre C, Séguin A, Hawkins S, Mackay J, Grima-Pettenati J. EgMYB1, an R2R3 MYB transcription factor from eucalyptus negatively regulates secondary cell wall formation in Arabidopsis and poplar. New Phytol 2010; 188:774-86. [PMID: 20955415 DOI: 10.1111/j.1469-8137.2010.03432.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
• The eucalyptus R2R3 transcription factor, EgMYB1 contains an active repressor motif in the regulatory domain of the predicted protein. It is preferentially expressed in differentiating xylem and is capable of repressing the transcription of two key lignin genes in vivo. • In order to investigate in planta the role of this putative transcriptional repressor of the lignin biosynthetic pathway, we overexpressed the EgMYB1 gene in Arabidopsis and poplar. • Expression of EgMYB1 produced similar phenotypes in both species, with stronger effects in transgenic Arabidopsis plants than in poplar. Vascular development was altered in overexpressors showing fewer lignified fibres (in phloem and interfascicular zones in poplar and Arabidopsis, respectively) and reduced secondary wall thickening. Klason lignin content was moderately but significantly reduced in both species. Decreased transcript accumulation was observed for genes involved in the biosynthesis of lignins, cellulose and xylan, the three main polymers of secondary cell walls. Transcriptomic profiles of transgenic poplars were reminiscent of those reported when lignin biosynthetic genes are disrupted. • Together, these results strongly suggest that EgMYB1 is a repressor of secondary wall formation and provide new opportunities to dissect the transcriptional regulation of secondary wall biosynthesis.
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Affiliation(s)
- Sylvain Legay
- UMR 5546, CNRS-UPS Surfaces Cellulaires et Signalisation chez les Végétaux, Castanet-Tolosan, France
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Rengel D, Clemente HS, Servant F, Ladouce N, Paux E, Wincker P, Couloux A, Sivadon P, Grima-Pettenati J. A new genomic resource dedicated to wood formation in Eucalyptus. BMC Plant Biol 2009; 9:36. [PMID: 19327132 PMCID: PMC2670833 DOI: 10.1186/1471-2229-9-36] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 03/27/2009] [Indexed: 05/17/2023]
Abstract
BACKGROUND Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource. RESULTS We report here the normalization and sequencing of a cDNA library from developing Eucalyptus secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile versus mature wood and vice versa). A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg) and 1,396 singletons (Sg) that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, Arabidopsis and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO) and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset. CONCLUSION In this work, we have identified a large set of wood-related Eucalyptus unigenes called EUCAWOOD, thus creating a valuable resource for functional genomics studies of wood formation and molecular breeding in this economically important genus. This set of publicly available annotated sequences will be instrumental for candidate gene approaches, custom array development and marker-assisted selection programs aimed at improving and modulating wood properties.
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Affiliation(s)
- David Rengel
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Hélène San Clemente
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Florence Servant
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : Syngenta Seeds SAS, BP27, 31790 Saint Sauveur, France
| | - Nathalie Ladouce
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
| | - Etienne Paux
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : INRA-UBP, UMR 1095, INRA Site de Crouël, 234 avenue du Brézet, 63100 Clermont-Ferrand, France
| | - Patrick Wincker
- Génoscope, CNRS, UMR 8030 and Université d'Evry, 91057 Evry, France
| | - Arnaud Couloux
- Génoscope, CNRS, UMR 8030 and Université d'Evry, 91057 Evry, France
| | - Pierre Sivadon
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
- Current address : Université de Pau et des Pays de l'Adour, UMR CNRS 5254 IPREM, IBEAS – BP1155, 64013 Pau Cedex, France
| | - Jacqueline Grima-Pettenati
- UMR CNRS/Université Toulouse III 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617 Auzeville, 31326 Castanet Tolosan, France
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Foucart C, Paux E, Ladouce N, San-Clemente H, Grima-Pettenati J, Sivadon P. Transcript profiling of a xylem vs phloem cDNA subtractive library identifies new genes expressed during xylogenesis in Eucalyptus. New Phytol 2006; 170:739-52. [PMID: 16684235 DOI: 10.1111/j.1469-8137.2006.01705.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Eucalyptus is one of the world's main sources of biomass. The genus includes species representing the principle hardwood trees used for pulp and paper. Here, we aimed to identify genes specifically expressed in differentiating secondary xylem compared with phloem. We constructed a xylem vs phloem subtractive library (Xp) that generated 263 unique sequences. By transcript profiling of xylem, phloem, vascular cambium and leaves using macroarrays, we classified the 263 unigenes into distinct tissue-specific groups. Reverse transcription-polymerase chain reaction (RT-PCR) confirmed the differential expression of representative expressed sequence tags (ESTs). A total of 87 unigenes were preferentially expressed in xylem. They were involved in functional categories known to play roles in xylogenesis, such as hormone signaling and metabolism, secondary cell wall thickening and proteolysis. Some of these genes, including unknown genes, may be considered xylem-specific and they are likely to control important functions in xylogenesis. These data shed light on the cellular functions of xylem cells and, importantly, provide us with a portfolio of Eucalyptus xylem genes that may be major players in the control of wood formation and quality.
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Affiliation(s)
- Camille Foucart
- UMR 5546 CNRS/Université Paul Sabatier Toulouse III, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP 42617 Auzeville Tolosane, 31326 Castanet Tolosan, France
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Ben C, Hewezi T, Jardinaud MF, Bena F, Ladouce N, Moretti S, Tamborindeguy C, Liboz T, Petitprez M, Gentzbittel L. Comparative analysis of early embryonic sunflower cDNA libraries. Plant Mol Biol 2005; 57:255-270. [PMID: 15821881 DOI: 10.1007/s11103-004-7532-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 12/12/2004] [Indexed: 05/24/2023]
Abstract
To gain information concerning cell functions and activities during sunflower embryogenesis, an expressed sequence tag (EST) approach was used to analyse gene expression in the early stages of sunflower embryos development. Confocal microscopy observations of whole-mounted embryos allowed us to identify precisely the major steps of the zygotic embryonic development. A time-course analysis was then employed to collect the embryonic material. Three cDNA libraries were constructed from microdissected embryos, and three other cDNA libraries were created using a classical day after pollination schedule. A total of 7106 ESTs were produced and assembled. The total number of putative different genes represents about 43.1 (3064 tentative contigs and singlets) of the analysed sequences. The unigenes that showed similarity to proteins with known or predicted functions (50.3) were classified into 15 different functional categories. The functional profiles were found to be quite similar for all studied embryo stages but statistical analysis revealed that successive and coordinate sets of genes are expressed at each embryonic stage. The analysis allowed us to identify abundant and differentially expressed genes at the early stages of embryos development as well as some putatively interesting genes, showing strong similarities with genes playing key roles in plant and animal embryogenesis. The data presented in this study not only provide a first global overview of the genes expression profile during sunflower embryogenesis but also represent an original and valuable tool for developmental genomics studies on exalbuminous dicots.
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Affiliation(s)
- Cécile Ben
- Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure de Toulouse, IFR40, 18 Chemin de Borde Rouge, 31326 Castanet Tolosan, France
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Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J. Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol Biol 2004; 55:263-280. [PMID: 15604680 DOI: 10.1007/s11103-004-0621-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wood is the most abundant biological resource on earth and it is also an important raw material for a major global industry with rapidly increasing demand. The genus Eucalyptus includes the most widely used tree species for industrial plantation, mainly for making pulp and paper. With the aim of identifying major genes involved in wood formation in Eucalyptus , we have developed a targeted approach of functional genomics based on the isolation of xylem preferentially expressed genes by subtractive PCR. Transcript profiling using cDNA arrays and analysis of variance (ANOVA) were used to identify differentially expressed ESTs between secondary xylem and leaves. Real-time RT-PCR was performed to confirm the differential expression of representative EST. Of 224 independent EST sequences obtained, 81% were preferentially expressed in xylem. One-third of the ESTs exhibiting homologies with proteins of known function fell into two main classes highlighting the importance of the auxin signalling through ubiquitin-dependent proteolysis on one hand, and of the enzymes involved in cell wall biosynthesis and remodelling, on the other. The functions of the genes represented by the remaining 61% of ESTs should be of great interest for future research. This systematic analysis of genes involved in wood formation in Eucalyptus provides valuable insights into the molecular mechanisms involved in secondary xylem differentiation as well as new candidate-genes for wood quality improvement.
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Affiliation(s)
- Etienne Paux
- UMR UPS/CNRS 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP17, Auzeville Tolosane, 31326 Castanet Tolosan, France
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