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Castric V, Batista RA, Carré A, Mousavi S, Mazoyer C, Godé C, Gallina S, Ponitzki C, Theron A, Bellec A, Marande W, Santoni S, Mariotti R, Rubini A, Legrand S, Billiard S, Vekemans X, Vernet P, Saumitou-Laprade P. The homomorphic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene. Curr Biol 2024; 34:1967-1976.e6. [PMID: 38626763 DOI: 10.1016/j.cub.2024.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
In flowering plants, outcrossing is commonly ensured by self-incompatibility (SI) systems. These can be homomorphic (typically with many different allelic specificities) or can accompany flower heteromorphism (mostly with just two specificities and corresponding floral types). The SI system of the Oleaceae family is unusual, with the long-term maintenance of only two specificities but often without flower morphology differences. To elucidate the genomic architecture and molecular basis of this SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals and related them to a genetic map. The S-locus region proved to have a segregating 543-kb indel unique to one specificity, suggesting a hemizygous region, as observed in all distylous systems so far studied at the genomic level. Only one of the predicted genes in this indel region is found in the olive tree, Olea europaea, genome, also within a segregating indel. We describe complete association between the presence/absence of this gene and the SI types determined for individuals of seven distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the gibberellic acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses of the two specificities in different ways. Our results provide a unique example of a homomorphic SI system, where a single conserved gibberellin-related gene in a hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.
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Affiliation(s)
- Vincent Castric
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Rita A Batista
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Amélie Carré
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Soraya Mousavi
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Clément Mazoyer
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Chloé Ponitzki
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Anthony Theron
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Arnaud Bellec
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - William Marande
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Sylvain Santoni
- UMR DIAPC Diversité et adaptation des plantes cultivées, F-34398 Montpellier, France
| | - Roberto Mariotti
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Andrea Rubini
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Sylvain Legrand
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Xavier Vekemans
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Philippe Vernet
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
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Mota APZ, Dossa K, Lechaudel M, Cornet D, Mournet P, Santoni S, Lopez D, Chaïr H. Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata. BMC Genomics 2024; 25:248. [PMID: 38443859 PMCID: PMC10916269 DOI: 10.1186/s12864-024-10135-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. METHODS AND RESULTS Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. CONCLUSIONS The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.
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Affiliation(s)
- Ana Paula Zotta Mota
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
- Université Côte d'Azur, Institut Sophia Agrobiotech, INRAE, CNRS, Sophia Antipolis, PACA, 06903, France
| | - Komivi Dossa
- UMR AGAP, CIRAD, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France
| | - Mathieu Lechaudel
- UMR Qualisud, CIRAD, F97130, Capesterre-Belle-Eau, Guadeloupe, France
- QualiSud, Université Montpellier, Institut Agro, CIRAD, Avignon Université, Université de La Réunion, 34398, Montpellier, France
| | - Denis Cornet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - David Lopez
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
| | - Hana Chaïr
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
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Crayol E, Huneau F, Garel E, Mattei A, Santoni S, Pasqualini V, Re V. Socio-hydrogeological survey and assessment of organic pollutants to highlight and trace back pollution fluxes threatening a coastal groundwater-dependent ecosystem. Science of The Total Environment 2023; 898:165343. [PMID: 37422224 DOI: 10.1016/j.scitotenv.2023.165343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
Despite being a vector of pollution towards connected ecosystems, groundwater is often underestimated or not taken into account in management frameworks. To fill this gap, we propose to add socio-economic data to hydrogeological investigations to identify past and present pollution sources linked to human activities at watershed scale in order to forecast threats towards groundwater-dependent ecosystems (GDEs). The aim of this paper is to demonstrate, by a cross-disciplinary approach, the added value of socio-hydrogeological investigations to tackle anthropogenic pollution fluxes towards a GDE and to contribute to more sustainable management of groundwater resources. A survey combining chemical compounds analysis, data compilation, land use analysis and field investigations with a questionnaire was carried out on the Biguglia lagoon plain (France). Results show a pollution with a two-fold source, both agricultural and domestic, in all water bodies of the plain. The pesticide analysis reveals the presence of 10 molecules, including domestic compounds, with concentrations exceeding European groundwater quality standards for individual pesticides, as well as pesticides already banned for twenty years. On the basis of both the field survey and the questionnaire, agricultural pollution has been identified as very local highlighting the storage capacity of the aquifer, whereas domestic pollution is diffuse over the plain and attributed to sewage network effluents and septic tanks. Domestic compounds present shorter residence time within the aquifer highlighting continuous inputs, related to consumption habits of the population. Under the Water Framework Directive (WFD), member states are required to preserve the good ecological status, quality and quantity of water bodies. However, for GDEs it is difficult to achieve the 'good status' required without considering the groundwater's pollutant storage capacity and pollution legacy. To help resolve this issue, socio-hydrogeology has proved to be an efficient tool as well as for implementing effective protection measures for Mediterranean GDEs.
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Affiliation(s)
- E Crayol
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP 52, 20250 Corte, France; CNRS, UMR 6134, SPE, BP 52, 20250 Corte, France.
| | - F Huneau
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP 52, 20250 Corte, France; CNRS, UMR 6134, SPE, BP 52, 20250 Corte, France
| | - E Garel
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP 52, 20250 Corte, France; CNRS, UMR 6134, SPE, BP 52, 20250 Corte, France
| | - A Mattei
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP 52, 20250 Corte, France; CNRS, UMR 6134, SPE, BP 52, 20250 Corte, France
| | - S Santoni
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP 52, 20250 Corte, France; CNRS, UMR 6134, SPE, BP 52, 20250 Corte, France
| | | | - V Re
- Università di Pisa, Dipartimento di Scienze della Terra, Via Santa Maria 53, 56126 Pisa, Italy
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Santoni S, Garel E, Gillon M, Babic M, Spangenberg JE, Bomou B, Sebag D, Adatte T, van Geldern R, Pasqualini V, Mattei A, Huneau F. The role of groundwater in CO 2 production and carbon storage in Mediterranean peatlands: An isotope geochemistry approach. Sci Total Environ 2023; 866:161098. [PMID: 36587657 DOI: 10.1016/j.scitotenv.2022.161098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/28/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Peatlands are permanent wetlands recognized for ecosystem services such as biodiversity conservation and carbon storage capacity. Little information is available about their response to global change, the reason why most Earth system climate models consider a linear increase in the release of greenhouse gases (GHG), such as CO2, with increasing temperatures. Nevertheless, numerous studies suggest that an increase in the temperature may not imply a decrease in photosynthesis and carbon storage rates if water availability is sufficient, the latter being under the control of local hydrology mechanisms. Mediterranean peatlands well illustrate this fact. Since they are groundwater-dependent, they are hydrologically resilient to the strong seasonality of hydroclimatic conditions, especially during the summer drought. In the present study, we demonstrate that, even if such peatlands release CO2 into the atmosphere, they can maintain a carbon storage capacity. To this end, a geochemical study disentangles the origin and fate of carbon within a Mediterranean peatland at the watershed scale. Field parameters, major ions, dissolved organic and inorganic carbon content and associated δ13C values allow for characterizing the seasonality of hydrochemical mechanisms and carbon input from an alluvial aquifer (where rain, river, shallow, and deep groundwater flows are mixing) to the peatland. The inorganic and organic content of peat soil and δ13C values of total organic matter and CO2 complete the dataset, making it possible to provide arguments in favour of lower organic matter oxidation compared to primary production. Overall, this study highlights the groundwater role in the fluxes of CO2 at the peatland-atmosphere interface, and more broadly the need to understand the interactions between the water and carbon cycles to build better models of the future evolution of the global climate.
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Affiliation(s)
- S Santoni
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP52, 20250 Corte, France; CNRS, UMR 6134 SPE, BP52, 20250 Corte, France.
| | - E Garel
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP52, 20250 Corte, France; CNRS, UMR 6134 SPE, BP52, 20250 Corte, France
| | - M Gillon
- Avignon Université, UMR 1114 EMMAH, INRAE, 301 rue Baruch de Spinoza, BP21239, 84916 Avignon, France
| | - M Babic
- Avignon Université, UMR 1114 EMMAH, INRAE, 301 rue Baruch de Spinoza, BP21239, 84916 Avignon, France
| | - J E Spangenberg
- University of Lausanne, Institute of Earth Surface Dynamics (IDYST), Géopolis, 1022 Chavannes-près-Renens, Lausanne 1015, Switzerland
| | - B Bomou
- University of Lausanne, Institute of Earth Sciences (ISTE), Géopolis, 1022 Chavannes-près-Renens, Lausanne 1015, Switzerland
| | - D Sebag
- IFP Energies Nouvelles, Earth Sciences and Environmental Technologies Division, 1-4 Avenue du bois Préau, 92852 Rueil-Malmaison, France
| | - T Adatte
- University of Lausanne, Institute of Earth Sciences (ISTE), Géopolis, 1022 Chavannes-près-Renens, Lausanne 1015, Switzerland
| | - R van Geldern
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Geography and Geosciences, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
| | - V Pasqualini
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP52, 20250 Corte, France; CNRS, UMR 6134 SPE, BP52, 20250 Corte, France
| | - A Mattei
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP52, 20250 Corte, France; CNRS, UMR 6134 SPE, BP52, 20250 Corte, France
| | - F Huneau
- Université de Corse Pascal Paoli, Département d'Hydrogéologie, Campus Grimaldi, BP52, 20250 Corte, France; CNRS, UMR 6134 SPE, BP52, 20250 Corte, France
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5
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Marinello D, Palla I, Lorenzoni V, Andreozzi G, Pirri S, Ticciati S, Cannizzo S, Del Bianco A, Ferretti E, Santoni S, Turchetti G, Mosca M, Talarico R. Exploring disease perception in Behçet's syndrome: combining a quantitative and a qualitative study based on a narrative medicine approach. Orphanet J Rare Dis 2023; 18:58. [PMID: 36934245 PMCID: PMC10024433 DOI: 10.1186/s13023-023-02668-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/11/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND Behçet Syndrome (BS) has a significant psychological and social impact on patients, caregivers and families. The present study aims at exploring disease perception in BS patients, using both a co-designed survey and the narrative medicine (NM) approach. METHODS An ad-hoc questionnaire was co-designed by clinicians expert in BS, BS patients and caregivers and BS adult patients were invited to answer the online questionnaires. Cluster analysis was used to analyse data from the survey and to identify groups of patients with diverse disease perception. To further explore real-life perspectives, the stories of illness of a smaller group of adult BS patients were anonymously collected online and analysed by means of text, sentiment and qualitative analysis. RESULTS Two hundred and seven patients answered the survey and forty-three stories were collected. The cluster analysis highlighted that accepting or not the disease has a strong impact on the daily life, on how BS patients perceive themselves and in terms of hope for the future. The stories revealed that patients often address common issues, such as the long and complex journey faced from the disease onset until the BS diagnosis, which was strongly connected to the concept of time and perceived as an exhausting period of their lives. CONCLUSION To our knowledge, this is the first study that addressed disease perception also applying the NM principles in BS. The current perception that BS patients have of their disease should encourage the BS scientific and patient community in joining forces in order to improve the journey of BS patients.
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Affiliation(s)
- D Marinello
- Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, Via Roma 67, 56126, Pisa, Italy
| | - I Palla
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - V Lorenzoni
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - G Andreozzi
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - S Pirri
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - S Ticciati
- Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, Via Roma 67, 56126, Pisa, Italy
| | - S Cannizzo
- Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, Via Roma 67, 56126, Pisa, Italy
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - A Del Bianco
- Associazione S.I.M.B.A (Associazione Italiana Sindrome e Malattia di Behçet), Pontedera, Italy
| | - E Ferretti
- Associazione S.I.M.B.A (Associazione Italiana Sindrome e Malattia di Behçet), Pontedera, Italy
| | - S Santoni
- Associazione S.I.M.B.A (Associazione Italiana Sindrome e Malattia di Behçet), Pontedera, Italy
| | - G Turchetti
- Institute of Management, Scuola Superiore Sant'Anna, Pisa, Italy
| | - M Mosca
- Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, Via Roma 67, 56126, Pisa, Italy
- Rheumatology Unit, University of Pisa, Pisa, Italy
| | - R Talarico
- Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, Via Roma 67, 56126, Pisa, Italy.
- Rheumatology Unit, University of Pisa, Pisa, Italy.
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Bataillon T, Gauthier P, Villesen P, Santoni S, Thompson JD, Ehlers BK. From genotype to phenotype: Genetic redundancy and the maintenance of an adaptive polymorphism in the context of high gene flow. Evol Lett 2022; 6:189-202. [PMID: 35386834 PMCID: PMC8966474 DOI: 10.1002/evl3.277] [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: 04/23/2021] [Revised: 12/23/2021] [Accepted: 01/16/2022] [Indexed: 11/11/2022] Open
Abstract
A central question in evolution is how several adaptive phenotypes are maintained within a species. Theory predicts that the genetic determination of a trait, and in particular the amounts of redundancy in the mapping of genotypes to phenotypes, mediates evolutionary outcomes of phenotypic selection. In Mediterranean wild thyme, numerous discrete chemical phenotypes (chemotypes) occur in close geographic proximity. Chemotypes are defined by the predominant monoterpene produced by individual plants in their essential oil. In this study, we analyze the ecological genetics of six chemotypes nested within two well‐established chemical families (hereafter ecotypes). Ecotypes, and chemotypes within ecotypes, are spatially segregated, and their distributions track local differences in the abiotic environment. By combining population genomic, phenotypic, and environmental data from 700 individuals, we show how the genetics of ecotype determination mediates this evolutionary response. Variation in three terpene‐synthase loci explains variation in ecotype identity, with one single locus accounting for as much as 78% of this variation. Phenotypic selection combined with low segregating genotypic redundancy of ecotypes leaves a clear footprint at the genomic level: alleles associated with ecotype identity track environmental variation despite extensive gene flow. Different chemotypes within each ecotype differentially track environmental variation. Their identity is determined by multiple loci and displays a wider range of genotypic redundancy that dilutes phenotypic selection on their characteristic alleles. Our study thus provides a novel illustration of how genetic redundancy of a phenotype modulates the ability of selection to maintain adaptive differentiation. Identifying the precise genetics of the chemical polymorphism in thyme is the next crucial step for our understanding of the origin and maintenance of a polymorphism that is present in many aromatic plants.
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Affiliation(s)
- Thomas Bataillon
- Bioinformatics Research Center Aarhus University Aarhus 8000 Denmark
| | - Perrine Gauthier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier 34293 France
| | - Palle Villesen
- Bioinformatics Research Center Aarhus University Aarhus 8000 Denmark
| | - Sylvain Santoni
- UMR AGAP Institut Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier 34398 France
| | - John D. Thompson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier 34293 France
| | - Bodil K. Ehlers
- Department of Ecoscience Aarhus University Silkeborg 8600 Denmark
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7
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Santoni S, Garel E, Gillon M, Marc V, Miller J, Babic M, Simler R, Travi Y, Leblanc M, Huneau F. Assessing the hydrogeological resilience of a groundwater-dependent Mediterranean peatland: Impact of global change and role of water management strategies. Sci Total Environ 2021; 768:144721. [PMID: 33454491 DOI: 10.1016/j.scitotenv.2020.144721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/04/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Mediterranean peatlands remain largely under-documented, except for detailed biological data such as fauna and flora taxa lists, and yet are increasingly threatened by water withdrawal and agriculture practices. This lack of information, particularly on their hydrogeological functioning, makes it impossible to evaluate their response to changing climate conditions. A pilot study on a representative Mediterranean peatland on the island of Corsica (France) was conducted to evaluate recharge modalities in the peatland using a coupled water-level monitoring, geochemical and isotope multi-tracing approach (electric conductivity, major ions, δ18O, δ2H, 3H, 87Sr/86Sr). The goal was to understand how water budgets in peatland ecosystems were maintained throughout the year, especially during the summer. Despite the remarkable stability of the peatland water level, the recharge contributions of varied water bodies through an alluvial aquifer vary significantly from one season to another. An end-member mixing analysis (EMMA) indicates that the peatland is mainly recharged by an alluvial aquifer. During fall-winter, the alluvial aquifer on which the peatland depends is recharged by the rainfall, a river, and shallow groundwater (colluvium). During spring-summer, water supply is provided mostly by a river, shallow, and deep groundwater (fractured granite). However, this specific hydrogeological functioning is not taken into account by environmental management policies making peatlands vulnerable to anthropogenic and climatic pressures. Thus, their actual status regarding water and aquatic environment management policies is discussed to provide recommendations for better consideration and preservation.
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Affiliation(s)
- S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France; Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France.
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - M Gillon
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - V Marc
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - J Miller
- Stellenbosch University, Department of Earth Sciences, Private Bag XI, Matieland 7602, South Africa
| | - M Babic
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - R Simler
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - Y Travi
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - M Leblanc
- Avignon Université, UMR 1114 EMMAH, UAPV, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
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8
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Juhlke TR, Van Geldern R, Barth JAC, Bendix J, Bräuning A, Garel E, Häusser M, Huneau F, Knerr I, Santoni S, Szymczak S, Trachte K. Temporal offset between precipitation and water uptake of Mediterranean pine trees varies with elevation and season. Sci Total Environ 2021; 755:142539. [PMID: 33045601 DOI: 10.1016/j.scitotenv.2020.142539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
For climate models that use paleo-environment data to predict future climate change, tree-ring isotope variations are one important archive for the reconstruction of paleo-hydrological conditions. Due to the rather complicated pathway of water, starting from precipitation until its uptake by trees and the final incorporation of its components into tree-ring cellulose, a closer inspection of seasonal variations of tree water uptake is important. In this study, branch and needle samples of two pine species (Pinus pinaster and Pinus nigra subsp. laricio) and several water compartments (precipitation, creek, soil) were sampled over a two-year period and analyzed for the temporal variations of their oxygen and hydrogen stable isotope ratios (δ18O and δ2H) at five sites over an elevation gradient from sea level to around 1600 m a.s.l. on the Mediterranean island of Corsica (France). A new model was established to disentangle temporal relationships of source water uptake of trees. It uses a calculation method that incorporates the two processes mostly expected to affect source water composition: mixing of waters and evaporation. The model results showed that the temporal offset from precipitation to water uptake is not constant and varies with elevation and season. Overall, seasonal source water origin was shown to be dominated by precipitation from autumn and spring. While autumn precipitation was a more important water source for trees growing at mid- (~800-1000 m a.s.l) and high-elevation (~1600 m a.s.l.) sites, trees at coastal sites mostly took up water from late winter and spring. These findings show that predicted decreases in precipitation amounts during the wet season in the Mediterranean can have strong impacts on water availability for pine trees, especially at higher elevations.
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Affiliation(s)
- T R Juhlke
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany.
| | - R Van Geldern
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
| | - J A C Barth
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
| | - J Bendix
- Philipps University of Marburg, Faculty of Geography, Laboratory for Climatology and Remote Sensing, Deutschhausstr. 12, 35032 Marburg, Germany
| | - A Bräuning
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, Institut für Geographie, Wetterkreuz 15, 91058 Erlangen, Germany
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - M Häusser
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, Institut für Geographie, Wetterkreuz 15, 91058 Erlangen, Germany
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - I Knerr
- Philipps University of Marburg, Faculty of Geography, Laboratory for Climatology and Remote Sensing, Deutschhausstr. 12, 35032 Marburg, Germany
| | - S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - S Szymczak
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, Institut für Geographie, Wetterkreuz 15, 91058 Erlangen, Germany
| | - K Trachte
- Brandenburg University of Technology (BTU), Institute for Environmental Sciences, 03044 Cottbus-Senftenberg, Germany
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9
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Kpatènon MJ, Salako KV, Santoni S, Zekraoui L, Latreille M, Tollon-Cordet C, Mariac C, Jaligot E, Beulé T, Adéoti K. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet 2020; 21:145. [PMID: 33272218 PMCID: PMC7713368 DOI: 10.1186/s12863-020-00955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00955-y.
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Affiliation(s)
- Mariano Joly Kpatènon
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kolawolé Valère Salako
- Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Laboratoire de Biomathématiques et d'Estimations Forestières (LABEF), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | | | - Estelle Jaligot
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Thierry Beulé
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Kifouli Adéoti
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin. .,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
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10
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Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
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Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
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11
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Tamisier L, Szadkowski M, Nemouchi G, Lefebvre V, Szadkowski E, Duboscq R, Santoni S, Sarah G, Sauvage C, Palloix A, Moury B. Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding. Mol Plant Pathol 2020; 21:3-16. [PMID: 31605444 PMCID: PMC6913244 DOI: 10.1111/mpp.12874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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Affiliation(s)
- Lucie Tamisier
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
- Present address:
Plant Pathology LaboratoryTERRA‐Gembloux Agro‐Bio TechUniversity of LiègePassage des Déportés, 25030GemblouxBelgium
| | - Marion Szadkowski
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
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12
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Amore Bonapasta S, Lazzaro S, Passafiume F, Santoni S, Grassi GB, Longo G. Laparoscopic management of acute, severe colon ischaemia: demanding emergency extended left hemicolectomy with completely intracorporeal anastomosis - a video vignette. Colorectal Dis 2019; 21:1454-1455. [PMID: 31390476 DOI: 10.1111/codi.14812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 02/08/2023]
Affiliation(s)
| | | | | | | | | | - G Longo
- Policlinico Casilino, Rome, Italy
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13
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. Plant J 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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14
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Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. Theor Appl Genet 2019; 132:2237-2252. [PMID: 31049634 DOI: 10.1007/s00122-019-03351-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 05/21/2023]
Abstract
A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.
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Affiliation(s)
- Javier Tello
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Catherine Roux
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Hajar Chouiki
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Valérie Laucou
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Audrey Weber
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Timothée Flutre
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Thierry Pons
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Patrice This
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France.
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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15
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Glémin S, Scornavacca C, Dainat J, Burgarella C, Viader V, Ardisson M, Sarah G, Santoni S, David J, Ranwez V. Pervasive hybridizations in the history of wheat relatives. Sci Adv 2019; 5:eaav9188. [PMID: 31049399 PMCID: PMC6494498 DOI: 10.1126/sciadv.aav9188] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/20/2019] [Indexed: 05/18/2023]
Abstract
Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought-Aegilops mutica, an overlooked wild species-instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.
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Affiliation(s)
- Sylvain Glémin
- CNRS, Univ Rennes, ECOBIO (Ecosystèmes, biodiversité, évolution)–UMR 6553, F-35042 Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier, cedex 05, France
| | - Jacques Dainat
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, S-751 23 Uppsala, Sweden
- IMBIM–Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, Box 582, S-751 23 Uppsala, Sweden
| | - Concetta Burgarella
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Véronique Viader
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Morgane Ardisson
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- South Green Bioinformatics Platform, BIOVERSITY, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jacques David
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Vincent Ranwez
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Bethune K, Mariac C, Couderc M, Scarcelli N, Santoni S, Ardisson M, Martin J, Montúfar R, Klein V, Sabot F, Vigouroux Y, Couvreur TLP. Long-fragment targeted capture for long-read sequencing of plastomes. Appl Plant Sci 2019; 7:e1243. [PMID: 31139509 PMCID: PMC6526642 DOI: 10.1002/aps3.1243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/21/2019] [Indexed: 05/09/2023]
Abstract
PREMISE Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. METHODS AND RESULTS The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. CONCLUSIONS Our protocol could also be generalized to capture long sequences from specific nuclear fragments.
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Affiliation(s)
| | | | | | | | - Sylvain Santoni
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | - Morgane Ardisson
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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17
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Jaunat J, Garel E, Huneau F, Erostate M, Santoni S, Robert S, Fox D, Pasqualini V. Combinations of geoenvironmental data underline coastal aquifer anthropogenic nitrate legacy through groundwater vulnerability mapping methods. Sci Total Environ 2019; 658:1390-1403. [PMID: 30677999 DOI: 10.1016/j.scitotenv.2018.12.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/03/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Groundwater quality is strongly dependent on land use. Past and current anthropogenic activities can lead to the diffusion of contaminants in aquifers. This diffusion can threaten the resource exploitation for decades, thereby endangering the ecological health of groundwater dependent ecosystems. Thus, groundwater stakeholders need methods for long-term management which integrate groundwater vulnerability. This study was conducted on the shallow alluvial aquifer of the groundwater-dependent Biguglia lagoon on Corsica Island, France. The aquifer is exposed to anthropogenic contamination for many decades with nitrate contamination legacy linked to agricultural activities, uncontrolled urbanization and sewage leakages. In most cases, vulnerability mapping is done in the objective of comparing groundwater situation regarding an on-going contamination process. But the question is still pending for aquifers where contamination is inherited from past practices or contaminations and where anthropogenic influences have changed through time. To propose an effective and innovative method for territorial management in Mediterranean alluvial aquifers, four index-based groundwater vulnerability mapping methods were tested and compared: two intrinsic vulnerability mapping methods (DRASTIC and SINTACS) and two specific vulnerability mapping methods (Modified-DRASTIC and SI), the latter integrating land use in the accuracy of groundwater vulnerability. Novelty is coming from the comparison between vulnerability maps and their application and validation in a hydrosystem affected by nitrate legacy-type contamination. The specific vulnerability mapping methods are more likely to represent the current pressures to which groundwater are subject. Thus, specific vulnerability methods such as the SI one revealed here very relevant to assess groundwater quality and to react retrospectively. The comparison between groundwater nitrate legacy and intrinsic groundwater vulnerability methods appeared also useful to define priority protection areas in long-term territorial management planning (EU Water Framework Direction). In this sense, the SINTACS method seems to be the more appropriate in the Mediterranean and alluvial context of this study.
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Affiliation(s)
- J Jaunat
- Université de Reims Champagne-Ardenne, EA 3795 - GEGENAA, 2 esplanade Roland Garros, F-51100 Reims, France.
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - M Erostate
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Département d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - S Robert
- Aix Marseille Université, Université Côte d'Azur, Avignon Université, UMR ESPACE 7300 CNRS, Avignon, France
| | - D Fox
- Université Côte d'Azur, UMR ESPACE 7300 CNRS, Nice, France
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18
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Juhlke TR, Van Geldern R, Huneau F, Garel E, Santoni S, Hemmerle H, Barth JAC. Riverine carbon dioxide evasion along a high-relief watercourse derived from seasonal dynamics of the water-atmosphere gas exchange. Sci Total Environ 2019; 657:1311-1322. [PMID: 30677898 DOI: 10.1016/j.scitotenv.2018.12.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The high-relief catchment of the Tavignanu River (Corsica Island, France) with an elevation range from sea level to 2622 m above sea level was investigated for its riverine carbon budget and stable carbon isotopes. Major riverine dissolved inorganic carbon (DIC or TCO2) sources depended on seasons and sub-catchment lithology. In winter δ13CDIC values of -2 to -7‰ (VPDB) indicated influences of atmospheric CO2. δ13CDIC values decreased gradually to values between -9 and -12‰ in July, which indicates elevated soil CO2 contribution. An observed downstream increase in the total amount of carbon species correlated with inputs from carbonate bearing tributaries and evaporation effects in summer. Main channel partial pressure of CO2 (pCO2) was seasonally highly variable in the upper silicate catchment and the lower coastal plain, where summer values exceed up to six times atmospheric levels. During winter, the central section of the Tavignanu River was found to be undersaturated with respect to atmospheric CO2 levels. The median values for main channel pCO2 were below atmospheric levels in winter and spring and above in summer and autumn. The annual carbon flux across the air-water boundary (FCO2) along the Tavignanu River was calculated with (0.77 ± 0.24) Gg C yr-1, which is about seven times higher than the riverine TCO2 transport to the sea of about 0.11 Gg C yr-1. While large sections of the river experienced year-round atmospheric CO2 uptake or equilibrium, the river as a whole was a small but continuous net source of carbon to the atmosphere. This underlines the important, but so far not well-constrained, contributions of smaller streams and rivers to the terrestrial carbon flux and the need of incorporating them into future global carbon cycle models.
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Affiliation(s)
- T R Juhlke
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany.
| | - R Van Geldern
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134 SPE, F-20250 Corte, France
| | - H Hemmerle
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
| | - J A C Barth
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department Geographie und Geowissenschaften, GeoZentrum Nordbayern, Schlossgarten 5, 91054 Erlangen, Germany
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Erostate M, Huneau F, Garel E, Lehmann MF, Kuhn T, Aquilina L, Vergnaud-Ayraud V, Labasque T, Santoni S, Robert S, Provitolo D, Pasqualini V. Delayed nitrate dispersion within a coastal aquifer provides constraints on land-use evolution and nitrate contamination in the past. Sci Total Environ 2018; 644:928-940. [PMID: 30743890 DOI: 10.1016/j.scitotenv.2018.06.375] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 06/09/2023]
Abstract
Identifying sources of anthropogenic pollution, and assessing the fate and residence time of pollutants in aquifers is important for the management of groundwater resources, and the ecological health of groundwater dependent ecosystems. This study investigates anthropogenic contamination in the shallow alluvial aquifer of the Marana-Casinca, hydraulically connected to the Biguglia lagoon (Corsica, France). A multi-tracer approach, combining geochemical and environmental isotopic data (δ18O-H2O, δ2H-H2O, 3H, δ15N-NO3-, δ18O-NO3-, δ11B), and groundwater residence-time tracers (3H and CFCs) was carried out in 2016, and integrated with a study of land use evolution in the catchment during the last century. Groundwater NO3- concentrations, ranged between 2 mg/L and up to 30 mg/L, displaying the degradation of groundwater quality induced by anthropogenic activities (agricultural activities). Comparatively high δ15N-NO3- values (up to 19.7‰) in combination with δ11B values that were significantly lower (between 23‰ and 26‰) than the seawater background are indicative of sewage contamination. The ongoing deterioration of groundwater quality can be attributed to the uncontrolled urbanization development all over the alluvial plain, with numerous sewage leakages from the sanitation network and private sewage systems. Integration of contaminant and water-residence time data revealed a progressive accumulation of pollutants with time in the groundwater, particularly in areas with major anthropogenic pressure and slow dynamic groundwater flow. Our approach provides time-dependent insight into nitrogen pollution in the studied aquifer over the past decades, revealing a systematic change in the dominant NO3- source, from agricultural to sewage contamination. Yet, today's low groundwater quality is to large parts due to legacy pollution from land-use practices several decades ago, underlining the poor self-remediating capacity of this hydrosystem. Our results can be taken as warning that groundwater pollution that happened in the recent past, or today, may have dire impacts on the quality of groundwater-dependent ecosystems in the future.
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Affiliation(s)
- M Erostate
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France.
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - M F Lehmann
- University of Basel, Department of Environmental Sciences, Basel, 4056, Switzerland
| | - T Kuhn
- University of Basel, Department of Environmental Sciences, Basel, 4056, Switzerland
| | - L Aquilina
- Université de Rennes, OSUR, Plateforme Condate eau, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - V Vergnaud-Ayraud
- Université de Rennes, OSUR, Plateforme Condate eau, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - T Labasque
- Université de Rennes, OSUR, Plateforme Condate eau, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - S Robert
- Aix-Marseille Université, UMR CNRS 7300 ESPACE, Technopôle de l'environnement Arbois Méditerranée, BP 80, F-13545 Aix-en-Provence Cedex 4, France
| | - D Provitolo
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, Sophia Antipolis, F-06560 Valbonne, France
| | - V Pasqualini
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
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20
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Singh P, Gobbi A, Santoni S, Hansen LH, This P, Péros JP. Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean. Frontiers in Life Science 2018. [DOI: 10.1080/21553769.2018.1552628] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Prashant Singh
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Alex Gobbi
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Patrice This
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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21
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Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V, Jiménez-Gómez JM, Rigaill G, Causse M. Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J 2018; 96:635-650. [PMID: 30079488 DOI: 10.1111/tpj.14057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F1 hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F1 hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Renaud Duboscq
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Muriel Latreille
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Sylvain Santoni
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Matthieu Beukers
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Fréderique Bitton
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Justine Gricourt
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Charles Poncet
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Véronique Gautier
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - José M Jiménez-Gómez
- INRA, UMR1318, Institut Jean-Pierre Bourgin, AgroParisTech-INRA-CNRS, Route de Saint Cyr, Versailles, 78026, France
| | - Guillem Rigaill
- INRA, UMR8071, Laboratoire de Mathématiques et Modélisation d'Evry, Université d'Evry Val d'Essonne, ENSIIE-INRA-CNRS, Évry, 91037, France
| | - Mathilde Causse
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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Chesnaux R, Santoni S, Garel E, Huneau F. An Analytical Method for Assessing Recharge Using Groundwater Travel Time in Dupuit-Forchheimer Aquifers. Ground Water 2018; 56:986-992. [PMID: 29732535 DOI: 10.1111/gwat.12794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
An analytical solution to calculate the recharge of unconfined aquifers with Dupuit-Forchheimer type flow conditions is proposed. This solution is derived from an existing closed-form analytical solution initially developed to determine groundwater travel time when the recharge of the aquifer is known. This existing solution has been modified to determine recharge when groundwater travel time is known. An illustration is given with a field case example for the Bonifacio aquifer of the island of Corsica (France), in the Mediterranean. In this aquifer, previously established differences in groundwater residence time between two water samples were determined from anthropogenic atmospheric gas (chlorofluorocarbons and sulfur hexafluoride) measurements. The time difference is entered into the new analytical solution to determine recharge. The calculations yield a value of average recharge that agrees with the results obtained by several other methods that were presented in previous studies to assess the recharge of the Bonifacio aquifer. Also presented in this study is a sensitivity analysis of the new analytical solution, to quantify the influence of different parameters that control recharge: hydraulic conductivity, effective porosity and the groundwater travel time. This study illustrates how geochemical data can be combined with physical models to measure recharge. Such an approach could be adopted in other homogeneous aquifers worldwide that satisfy Dupuit-Forchheimer type flow conditions.
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Affiliation(s)
| | - S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250, Corte, France
- CNRS, UMR 6134, SPE, F-20250, Corte, France
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250, Corte, France
- CNRS, UMR 6134, SPE, F-20250, Corte, France
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250, Corte, France
- CNRS, UMR 6134, SPE, F-20250, Corte, France
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23
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Cruaud A, Gonzalez AA, Godefroid M, Nidelet S, Streito JC, Thuillier JM, Rossi JP, Santoni S, Rasplus JY. Using insects to detect, monitor and predict the distribution of Xylella fastidiosa: a case study in Corsica. Sci Rep 2018; 8:15628. [PMID: 30353142 PMCID: PMC6199265 DOI: 10.1038/s41598-018-33957-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022] Open
Abstract
We sampled ca 2500 specimens of Philaenus spumarius (Hemiptera: Aphrophoridae) throughout Corsica without a priori knowledge on the presence of symptoms on plants. We screened 448 specimens for the presence of Xylella fastidiosa (Xf) using qPCR and a custom nested PCR. qPCR appeared versatile and under-estimated the prevalence of Xf. Nested PCR showed that Xf was present in all populations. Molecular results were validated by prediction on the distribution of Xf made from tests conducted on plants, which shows the pertinence of using vectors in risk assessment studies. Xf was detected in tenerals and adults. Thus, P. spumarius could acquire Xf from its host plant, mostly Cistus monspeliensis in Corsica, which may act as reservoir for the next season. This contrasts with other observations and suggests that management strategies may have to be adapted on a case-by-case basis. At least two genetic entities and several variants of Xf not yet identified on plants were present in the insects, which suggests ancient introductions of Xf and a probable underestimation of the current diversity of the strains present in Corsica. Interestingly 6% of the specimens carried two subspecies of Xf. Studies are required to better characterize the strains present in Corsica and to determine how the disease was introduced, spread and why no sign of a potential epidemic was detected earlier. This study shows that, when sensitive enough methods are implemented, spittlebugs (and more specifically P. spumarius for which species distribution modelling shows it could be a good sentinel for Europe) can be used to predict and better assess the exact distribution of Xf. Furthermore, Xf multiply only in their foregut and does not become circulative, which facilitates its detection.
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France.
| | - Anne-Alicia Gonzalez
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
- INRA, UMR1334 AGAP, F-34398, Montpellier, France
| | - Martin Godefroid
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Sabine Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Jean-Claude Streito
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Jean-Marc Thuillier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Jean-Pierre Rossi
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | | | - Jean-Yves Rasplus
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
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Mollion M, Ehlers BK, Figuet E, Santoni S, Lenormand T, Maurice S, Galtier N, Bataillon T. Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes. Genome Biol Evol 2018; 10:239-248. [PMID: 29272394 PMCID: PMC5815141 DOI: 10.1093/gbe/evx272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied.
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Affiliation(s)
- Maeva Mollion
- Bioinformatics Research Center, Aarhus University, C.F. Møllers Alle 8, Building 1110, 8000 Aarhus C, Denmark
| | - Bodil K Ehlers
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark
| | - Emeric Figuet
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Sylvain Santoni
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, 1919, route de Mende 34293 Montpellier, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, 1919, route de Mende 34293 Montpellier, France
| | - Sandrine Maurice
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Thomas Bataillon
- Bioinformatics Research Center, Aarhus University, C.F. Møllers Alle 8, Building 1110, 8000 Aarhus C, Denmark
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Singh P, Santoni S, This P, Péros JP. Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine's Phyllosphere and Carposphere: An NGS Approach. Microorganisms 2018; 6:microorganisms6040096. [PMID: 30248973 PMCID: PMC6313654 DOI: 10.3390/microorganisms6040096] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 11/26/2022] Open
Abstract
Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors (i.e., at different geographic locations) on the phyllosphere has never been studied and is the main objective of this report. Using high throughput short amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS), we analyzed the impacts of genotypes of Vitis Vinifera (coming from three genetic pool), on the microbial (bacterial and fungal) assemblage in the phyllosphere. First, we performed the analysis of the phyllosphere microbiome while using fifteen genotypes that were chosen to maximize intra-specific diversity and grown in two Mediterranean vineyards. Then, the same analysis was performed on five commercially important varieties of Vitis vinifera that were sampled from three different French agro-climatic zones (or terroir: a combination of climate, soils, and human practices). Our study revealed that, at a particular geographic location, genotypes have an impact on microbial assemblage in the phyllosphere and carposphere of leaf and fruit (or berries), respectively, which is more prominent on the carposphere but the effect of terroir was much stronger than the genotype when the leaf phyllosphere of five grapevine varieties grown in different agro-climatic zones was compared. Impacts of the season and exterior plant organs (leaf and berries) on microbial taxa structuring in the phyllosphere was also assessed and presented in this report.
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Affiliation(s)
- Prashant Singh
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34000 Montpellier, France.
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34000 Montpellier, France.
| | - Patrice This
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34000 Montpellier, France.
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34000 Montpellier, France.
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Salomez M, Subileau M, Vallaeys T, Santoni S, Bonfils F, Sainte-Beuve J, Intapun J, Granet F, Vaysse L, Dubreucq É. Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber. J Appl Microbiol 2018; 124:444-456. [PMID: 29222942 DOI: 10.1111/jam.13661] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/03/2017] [Accepted: 11/29/2017] [Indexed: 11/29/2022]
Abstract
AIM To characterize microbial communities present in natural rubber (NR) coagula from Hevea brasiliensis latex during maturation and identify microbial taxa (bacteria and fungi) having an impact on dry NR properties. METHODS AND RESULTS Microbial community dynamics in NR coagula maturated under controlled conditions were compared and related with the evolution of dry NR properties. The pyrosequencing of 16S (119 837 effective reads) and 18S (131 879 effective reads) rRNA gene regions was performed on 21 samples covering different maturation times and two aeration conditions. Results showed a relatively high bacterial richness (Chao1 estimates of 200-1000) associated with significant bacterial dynamics. Lactic acid bacteria (LAB) were dominant in the first days of maturation. Then, in aerobic conditions, development of Actinobacteria represented by the family Microbacteriaceae was associated with alkalinization of the samples and a higher sensitivity of NR to thermo-oxidation as evaluated by its plasticity retention index (PRI). In anaerobiosis, the reduced development of bacteria, mostly LAB present, was associated with improved NR properties (higher initial plasticity P0 and PRI). CONCLUSIONS The involvement of micro-organisms in the evolution of dry NR properties during the maturation of NR coagula was confirmed. The importance of the structure and dynamics of microbial communities is specifically highlighted. SIGNIFICANCE AND IMPACT OF THE STUDY Natural rubber is a key elastomer for the tyre industry and for a variety of other applications. The majority of raw NR is obtained by natural coagulation of H. brasiliensis latex under the activity of micro-organisms. An improved understanding of the microbial communities involved in the maturation of NR coagula may lead to an improvement in the production process of raw NR to provide a better consistency in NR quality.
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Affiliation(s)
- M Salomez
- UMR IATE, Montpellier SupAgro, Montpellier, France
| | - M Subileau
- UMR IATE, Montpellier SupAgro, Montpellier, France
| | - T Vallaeys
- UMR ECOSYM, Université de Montpellier, Montpellier, France
| | | | - F Bonfils
- UMR IATE, CIRAD, Montpellier, France
| | | | - J Intapun
- Surat Thani Campus, Prince of Songkla University, Surat Thani, Thailand
| | - F Granet
- MFP Michelin, Clermont-Ferrand, France
| | - L Vaysse
- UMR IATE, CIRAD, Montpellier, France
| | - É Dubreucq
- UMR IATE, Montpellier SupAgro, Montpellier, France
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27
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Rode NO, Holtz Y, Loridon K, Santoni S, Ronfort J, Gay L. How to optimize the precision of allele and haplotype frequency estimates using pooled-sequencing data. Mol Ecol Resour 2017; 18:194-203. [PMID: 28977733 DOI: 10.1111/1755-0998.12723] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 02/07/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 11/30/2022]
Abstract
Sequencing pools of individuals rather than individuals separately reduces the costs of estimating allele frequencies at many loci in many populations. Theoretical and empirical studies show that sequencing pools comprising a limited number of individuals (typically fewer than 50) provides reliable allele frequency estimates, provided that the DNA pooling and DNA sequencing steps are carefully controlled. Unequal contributions of different individuals to the DNA pool and the mean and variance in sequencing depth both can affect the standard error of allele frequency estimates. To our knowledge, no study separately investigated the effect of these two factors on allele frequency estimates; so that there is currently no method to a priori estimate the relative importance of unequal individual DNA contributions independently of sequencing depth. We develop a new analytical model for allele frequency estimation that explicitly distinguishes these two effects. Our model shows that the DNA pooling variance in a pooled sequencing experiment depends solely on two factors: the number of individuals within the pool and the coefficient of variation of individual DNA contributions to the pool. We present a new method to experimentally estimate this coefficient of variation when planning a pooled sequencing design where samples are either pooled before or after DNA extraction. Using this analytical and experimental framework, we provide guidelines to optimize the design of pooled sequencing experiments. Finally, we sequence replicated pools of inbred lines of the plant Medicago truncatula and show that the predictions from our model generally hold true when estimating the frequency of known multilocus haplotypes using pooled sequencing.
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Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S. Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant J 2017; 91:631-645. [PMID: 28488328 DOI: 10.1111/tpj.13592] [Citation(s) in RCA: 18] [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: 12/28/2016] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 05/25/2023]
Abstract
Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species.
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Affiliation(s)
- Christopher Sauvage
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Charlotte Aichholz
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Joël Chadoeuf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Gautier Sarah
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP, Baillarguet, F-34980, Montferrier-sur-Lez, France
| | - Sylvain Santoni
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Jacques David
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier (ISEM-UMR 5554 Université de Montpellier - CNRS-IRD-EPHE), F-34095, Montpellier, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
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Holtz Y, Bonnefoy M, Viader V, Ardisson M, Rode NO, Poux G, Roumet P, Marie-Jeanne V, Ranwez V, Santoni S, Gouache D, David JL. Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus. Theor Appl Genet 2017; 130:1491-1505. [PMID: 28451771 PMCID: PMC5487696 DOI: 10.1007/s00122-017-2904-6] [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: 10/14/2016] [Accepted: 03/27/2017] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.
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Affiliation(s)
- Yan Holtz
- Montpellier SupAgro, UMR AGAP, 34060, Montpellier, France.
| | - Michel Bonnefoy
- Montpellier SupAgro, UMR BGPI, 34398, Montpellier Cedex 5, France
| | | | | | | | | | | | | | - Vincent Ranwez
- Montpellier SupAgro, UMR AGAP, 34060, Montpellier, France
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Santoni S, Huneau F, Garel E, Aquilina L, Vergnaud-Ayraud V, Labasque T, Celle-Jeanton H. Strontium isotopes as tracers of water-rocks interactions, mixing processes and residence time indicator of groundwater within the granite-carbonate coastal aquifer of Bonifacio (Corsica, France). Sci Total Environ 2016; 573:233-246. [PMID: 27565532 DOI: 10.1016/j.scitotenv.2016.08.087] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/12/2016] [Accepted: 08/13/2016] [Indexed: 06/06/2023]
Abstract
This study aims at identifying the water-rock interactions and mixing rates within a complex granite-carbonate coastal aquifer under high touristic pressure. Investigations have been carried out within the coastal aquifer of Bonifacio (southern Corsica, France) mainly composed of continental granitic weathering products and marine calcarenite sediments filling a granitic depression. A multi-tracer approach combining physico-chemical parameters, major ions, selected trace elements, stable isotopes of the water molecule and 87Sr/86Sr ratios measurements is undertaken for 20 groundwater samples during the low water period in November 2014. 5 rock samples of the sedimentary deposits and surrounding granites are also analysed. First, the water-rock interactions processes governing the groundwater mineralization are described in order to fix the hydrogeochemical background. Secondly, the flow conditions are refined through the quantification of inter aquifer levels mixing, and thirdly, the kinetics of water-rock interaction based on groundwater residence time from a previous study using CFCs and SF6 are quantified for the two main flow lines. A regional contrast in the groundwater recharge altitude allowed the oxygene-18 to be useful combined with the 87Sr/86Sr ratios to differentiate the groundwater origins and to compute the mixing rates, revealing the real extension of the watershed and the availability of the resource. The results also highlight a very good correlation between the groundwater residence time and the spatial evolution of 87Sr/86Sr ratios, allowing water-rock interaction kinetics to be defined empirically for the two main flow lines through the calcarenites. These results demonstrate the efficiency of strontium isotopes as tracers of water-rock interaction kinetics and by extension their relevance as a proxy of groundwater residence time, fundamental parameter documenting the long term sustainability of the hydrosystem.
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Affiliation(s)
- S Santoni
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France.
| | - F Huneau
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - E Garel
- Université de Corse Pascal Paoli, Faculté des Sciences et Techniques, Laboratoire d'Hydrogéologie, Campus Grimaldi, BP 52, F-20250 Corte, France; CNRS, UMR 6134, SPE, F-20250 Corte, France
| | - L Aquilina
- OSUR, Géosciences Rennes, UMR 6118, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - V Vergnaud-Ayraud
- OSUR, Géosciences Rennes, UMR 6118, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - T Labasque
- OSUR, Géosciences Rennes, UMR 6118, CNRS/Université Rennes-1, F-35042 Rennes, France
| | - H Celle-Jeanton
- Université de Bourgogne Franche-Comté, UFR Sciences et Techniques, CNRS UMR 6249 Chrono-Environnement, 16 route de Gray, F-25 030 Besançon Cedex, France
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31
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Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Mol Ecol Resour 2016; 17:565-580. [PMID: 27487989 DOI: 10.1111/1755-0998.12587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 09/23/2014] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 12/20/2022]
Abstract
We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.
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Affiliation(s)
| | - Felix Homa
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | | | | | - Benoit Nabholz
- Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France
| | | | - Laure Sauné
- INRA, UMR AGAP, F-34060, Montpellier, France
| | | | | | - Christopher Sauvage
- INRA, UR1052, GAFL, 67 allée des Chênes Domaine Saint Maurice- CS60094, 84143, Montfavet Cedex, France
| | | | - Cyril Jourda
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | - Hana Chair
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | - Claire Billot
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | | | - Michel Boccara
- CIRAD/CRC, UMR AGAP, UWI, St Augustine, Trinidad and Tobago
| | | | | | | | | | - Jacques David
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.,CIAT, Recta Cali Palmira km 17, Cali, Colombia
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Bataillon T, Galtier N, Bernard A, Cryer N, Faivre N, Santoni S, Severac D, Mikkelsen TN, Larsen KS, Beier C, Sørensen JG, Holmstrup M, Ehlers BK. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate. Glob Chang Biol 2016; 22:2370-2379. [PMID: 27109012 PMCID: PMC5021122 DOI: 10.1111/gcb.13293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/15/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.
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Affiliation(s)
- Thomas Bataillon
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Galtier
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Aurelien Bernard
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Nicolai Cryer
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Faivre
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | | | - Dany Severac
- c/o Institut de Génomique FonctionnelleMGX‐Montpellier GenomiX34094 Montpellier Cedex 05France
| | - Teis N. Mikkelsen
- Department of Chemical and Biochemical EngineeringEcosystems CentreTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Klaus S. Larsen
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
| | - Claus Beier
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
- Centre for Catchments and Urban Water ResearchNorwegian Institute for Water Research (NIVA)Gaustadalléen 210349OsloNorway
| | - Jesper G. Sørensen
- Department of BioscienceAarhus UniversityNy Munkegade 1168000Aarhus CDenmark
| | - Martin Holmstrup
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
| | - Bodil K. Ehlers
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
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Zehdi-Azouzi S, Cherif E, Guenni K, Abdelkrim AB, Bermil A, Rhouma S, Salah MB, Santoni S, Pintaud JC, Aberlenc-Bertossi F, Hannachi AS. Endemic insular and coastal Tunisian date palm genetic diversity. Genetica 2016; 144:181-90. [PMID: 26895027 DOI: 10.1007/s10709-016-9888-z] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/14/2016] [Indexed: 11/30/2022]
Abstract
The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.
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Affiliation(s)
- Salwa Zehdi-Azouzi
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia.
| | - Emira Cherif
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia.,IRD, UMR DIADE F2F and DYNADIV Teams, 911 Av. Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Karim Guenni
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia
| | - Ahmed Ben Abdelkrim
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia
| | - Aymen Bermil
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia
| | - Soumaya Rhouma
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia
| | - Mohamed Ben Salah
- Centre Régional de Recherche en Agriculture Oasienne, 2260, Degueche, Tunisia
| | - Sylvain Santoni
- INRA, UMR 1097 Diversité et Adaptation des Plantes Cultivées, 2 Place Viala, 34060, Montpellier Cedex 1, France
| | - Jean Christophe Pintaud
- IRD, UMR DIADE F2F and DYNADIV Teams, 911 Av. Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Amel Salhi Hannachi
- Laboratoire de génétique moléculaire immunologie et biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunis, Tunisia
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Zehdi-Azouzi S, Cherif E, Moussouni S, Gros-Balthazard M, Abbas Naqvi S, Ludeña B, Castillo K, Chabrillange N, Bouguedoura N, Bennaceur M, Si-Dehbi F, Abdoulkader S, Daher A, Terral JF, Santoni S, Ballardini M, Mercuri A, Ben Salah M, Kadri K, Othmani A, Littardi C, Salhi-Hannachi A, Pintaud JC, Aberlenc-Bertoss F. Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations. Ann Bot 2015; 116:847. [PMID: 26378059 PMCID: PMC4590333 DOI: 10.1093/aob/mcv132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Since the publication of this paper, it has become apparent that an error was made in the legend to Fig. 3 and the colours referring to occidental and oriental are the wrong way round. The authors apologise for this error, and a correct version of the legend to Fig. 3 is given below.
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Zehdi-Azouzi S, Cherif E, Moussouni S, Gros-Balthazard M, Abbas Naqvi S, Ludeña B, Castillo K, Chabrillange N, Bouguedoura N, Bennaceur M, Si-Dehbi F, Abdoulkader S, Daher A, Terral JF, Santoni S, Ballardini M, Mercuri A, Ben Salah M, Kadri K, Othmani A, Littardi C, Salhi-Hannachi A, Pintaud JC, Aberlenc-Bertossi F. Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations. Ann Bot 2015; 116:101-12. [PMID: 26113618 PMCID: PMC4479755 DOI: 10.1093/aob/mcv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 04/13/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. METHODS Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. KEY RESULTS Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. CONCLUSIONS This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.
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Affiliation(s)
- Salwa Zehdi-Azouzi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Emira Cherif
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Souhila Moussouni
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Muriel Gros-Balthazard
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Summar Abbas Naqvi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Bertha Ludeña
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe D
| | - Karina Castillo
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Nathalie Chabrillange
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Nadia Bouguedoura
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Malika Bennaceur
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Farida Si-Dehbi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Sabira Abdoulkader
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Abdourahman Daher
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Jean-Frederic Terral
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Sylvain Santoni
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Marco Ballardini
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Antonio Mercuri
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Mohamed Ben Salah
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Karim Kadri
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Ahmed Othmani
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Claudio Littardi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Amel Salhi-Hannachi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Jean-Christophe Pintaud
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
| | - Frédérique Aberlenc-Bertossi
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus universitaire El Manar, 2092, Tunisia, IRD, UMR DIADE-F2F, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France, Université des Sciences et de la Technologie Houari Boumediene (USTHB), Laboratoire de Recherche sur les Zones Arides (LRZA), BP 32 Bab Ezzouar-El Alia, 16111, Alger, Algeria, Institut des Sciences de l'Evolution de Montpellier, UMR 5554, équipe Dynamique de la biodiversité, anthropo-écologie, Place Eugène Bataillon, CC 065, 34095 Montpellier cedex 05, France, Institute of Horticultural Sciences, University of Agriculture, 38040 Faisalabad, Pakistan, School of Biology, Yachay-Tech, Yachay City of Knowledge, 100119 Urcuqui, Ecuador, Université Oran1-Ahmed Ben Bella, Faculté des sciences de la nature et de la vie, Département de Biologie, BP 1524 El Mnaouar, 31000 Oran, Algérie, ISV/CERD, route de l'Aéroport, BP 486, Djibouti, INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France, Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy, Centre Régional de Recherche en Agriculture Oasienne, 2260 Degueche, Tunisia and Centro Studi e Ricerche per le Palme, Corso F. Cavallotti 113, 18038 Sanremo (IM), Italy
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Clermont D, Santoni S, Saker S, Gomard M, Gardais E, Bizet C. Assessment of DNA encapsulation, a new room-temperature DNA storage method. Biopreserv Biobank 2015; 12:176-83. [PMID: 24955733 DOI: 10.1089/bio.2013.0082] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A new procedure for room-temperature storage of DNA was evaluated whereby DNA samples from human tissue, bacteria, and plants were stored under an anoxic and anhydrous atmosphere in small glass vials fitted in stainless-steel, laser-sealed capsules (DNAshells(®)). Samples were stored in DNAshells(®) at room temperature for various periods of time to assess any degradation and compare it to frozen control samples and those stored in GenTegra™ tubes. The study included analysis of the effect of accelerated aging by using a high temperature (76°C) at 50% relative humidity. No detectable DNA degradation was seen in samples stored in DNAshells(®) at room temperature for 18 months. Polymerase chain reaction experiments, pulsed field gel electrophoresis, and amplified fragment length polymorphism analyses also demonstrated that the protective properties of DNAshells(®) are not affected by storage under extreme conditions (76°C, 50% humidity) for 30 hours, guaranteeing 100 years without DNA sample degradation. However, after 30 hours of storage at 76°C, it was necessary to include adjustments to the process in order to avoid DNA loss. Successful protection of DNA was obtained for 1 week and even 1 month of storage at high temperature by adding trehalose, which provides a protective matrix. This study demonstrates the many advantages of using DNAshells(®) for room-temperature storage, particularly in terms of long-term stability, safety, transport, and applications for molecular biology research.
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Affiliation(s)
- Dominique Clermont
- 1 Institut Pasteur, Collection de l'Institut Pasteur , Département de Microbiologie, Paris, France
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Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R. A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC Plant Biol 2014; 14:229. [PMID: 25179565 PMCID: PMC4167142 DOI: 10.1186/s12870-014-0229-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 04/10/2014] [Accepted: 08/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinifera. The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus Vitis, sex determination is putatively controlled by one major locus with three alleles, male M, hermaphrodite H and female F, with an allelic dominance M > H > F. Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse V. vinifera genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism. RESULTS In V. v. sylvestris, a sex-determining region of 154.8 kb, also present in other Vitis species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a trehalose phosphatase, an exostosin and a WRKY transcription factor, with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that H alleles are more closely related to M than to F alleles. CONCLUSIONS Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian Vitis species into the cultivated grapevine gene pool.
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Affiliation(s)
- Sandrine Picq
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Sylvain Santoni
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Thierry Lacombe
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Muriel Latreille
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Audrey Weber
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Morgane Ardisson
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Sarah Ivorra
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - David Maghradze
- />Institute of Horticulture, Viticulture and Oenology, Agrarian University of Georgia, University Campus at Digomi, David Aghmashenebeli Alley, 13-th km. 0159, Tbilisi, Georgia
| | - Rosa Arroyo-Garcia
- />CBGP-INIA. Dpto Biotecnología, Campus de Montegancedo, Autovía M40, km38, 28223 Pozuelo de Alarcón, Madrid Spain
| | - Philippe Chatelet
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Patrice This
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Jean-Frédéric Terral
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
- />Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
| | - Roberto Bacilieri
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
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Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur TLP. Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Resour 2014; 14:1103-13. [DOI: 10.1111/1755-0998.12258] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Cédric Mariac
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Nora Scarcelli
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Juliette Pouzadou
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Adeline Barnaud
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Laboratoire National de Recherche sur les Productions Végétales; Institut Sénégalais de Recherches Agricoles; Centre de Recherche de Bel Air; Dakar Senegal
- Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux; Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop; Centre de Recherche de Bel Air; Dakar Senegal
| | | | - Adama Faye
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
| | - Ayite Kougbeadjo
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Vincent Maillol
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | | | - François Sabot
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Sylvain Santoni
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Thomas L. P. Couvreur
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
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Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Mol Ecol 2014; 23:2210-27. [PMID: 24684265 DOI: 10.1111/mec.12738] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [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: 11/25/2013] [Accepted: 03/19/2014] [Indexed: 12/17/2022]
Abstract
The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.
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Affiliation(s)
- Benoit Nabholz
- Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France; UMR AGAP 1334, Montpellier SupAgro, Montpellier, France
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Aberlenc-Bertossi F, Castillo K, Tranchant-Dubreuil C, Chérif E, Ballardini M, Abdoulkader S, Gros-Balthazard M, Chabrillange N, Santoni S, Mercuri A, Pintaud JC. In silico mining of microsatellites in coding sequences of the date palm (Arecaceae) genome, characterization, and transferability. Appl Plant Sci 2014; 2:apps1300058. [PMID: 25202594 PMCID: PMC4123382 DOI: 10.3732/apps.1300058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/24/2013] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. • METHODS AND RESULTS Tandem repeat motifs of 3-6 bp were searched using a simple sequence repeat (SSR)-pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. • CONCLUSIONS These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.
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Affiliation(s)
- Frédérique Aberlenc-Bertossi
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
- Author for correspondence:
| | - Karina Castillo
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
| | | | - Emira Chérif
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
- Laboratoire de génétique moléculaire, immunologie et biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 El Manar, Tunis, Tunisia
| | - Marco Ballardini
- Consiglio per la ricerca e la sperimentazione in agricoltura—Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy
| | - Sabira Abdoulkader
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
- ISV/CERD, route de l’Aéroport, BP 468, Djibouti
| | - Muriel Gros-Balthazard
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
- Centre de Bio-Archéologie et d’Ecologie (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP), Institut de Botanique, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| | - Nathalie Chabrillange
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
| | - Sylvain Santoni
- INRA, UMR AGAP, 2 Place Viala, 34060 Montpellier, Cedex 1, France
| | - Antonio Mercuri
- Consiglio per la ricerca e la sperimentazione in agricoltura—Unità di Ricerca per la Floricoltura e le Specie Ornamentali (CRA-FSO), Corso degli Inglesi 508, I-18038 Sanremo (IM), Italy
| | - Jean-Christophe Pintaud
- IRD, UMR DIADE—BDP, DYNADIV, and EVODYN teams, 911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
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Tonnabel J, Olivieri I, Mignot A, Rebelo A, Justy F, Santoni S, Caroli S, Sauné L, Bouchez O, Douzery EJP. Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach. Mol Phylogenet Evol 2013; 70:37-46. [PMID: 23948865 DOI: 10.1016/j.ympev.2013.07.027] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 07/12/2013] [Accepted: 07/29/2013] [Indexed: 01/30/2023]
Abstract
Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3' untranslated regions (3'-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3'-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3'-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3'-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.
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Affiliation(s)
- Jeanne Tonnabel
- Université Montpellier 2, CNRS, Institut des Sciences de l'Évolution (UMR 5554), Place Eugène Bataillon, 34095 Montpellier cedex 05, France.
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Pintaud JC, Ludeña B, Aberlenc-Bertossi F, Zehdi S, Gros-Balthazard M, Ivorra S, Terral JF, Newton C, Tengberg M, Abdoulkader S, Daher A, Nabil M, Saro Hernández I, González-Pérez M, Sosa P, Santoni S, Moussouni S, Si-Dehbi F, Bouguedoura N. BIOGEOGRAPHY OF THE DATE PALM (PHOENIX DACTYLIFERA L., ARECACEAE): INSIGHTS ON THE ORIGIN AND ON THE STRUCTURE OF MODERN DIVERSITY. ACTA ACUST UNITED AC 2013. [DOI: 10.17660/actahortic.2013.994.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bobadilla Landey R, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J, Etienne H. High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS One 2013; 8:e56372. [PMID: 23418563 PMCID: PMC3572038 DOI: 10.1371/journal.pone.0056372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 10/29/2012] [Accepted: 01/08/2013] [Indexed: 01/30/2023] Open
Abstract
Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee.
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Affiliation(s)
- Roberto Bobadilla Landey
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Alberto Cenci
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Frédéric Georget
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Benoît Bertrand
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Gloria Camayo
- Centro Nacional de Investigaciones de Café, Manizales, Colombia
| | - Eveline Dechamp
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | | | - Sylvain Santoni
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Tropicales et Méditerranéennes, Institut National de la Recherche Agronomique, Montpellier, France
| | - Philippe Lashermes
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - June Simpson
- Department of Plant Genetic Engineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Hervé Etienne
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
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Besnard G, Khadari B, Navascués M, Fernández-Mazuecos M, El Bakkali A, Arrigo N, Baali-Cherif D, Brunini-Bronzini de Caraffa V, Santoni S, Vargas P, Savolainen V. The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant. Proc Biol Sci 2013; 280:20122833. [PMID: 23390107 DOI: 10.1098/rspb.2012.2833] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.
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Affiliation(s)
- G Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse Cedex 9, France.
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Cherif E, Zehdi S, Castillo K, Chabrillange N, Abdoulkader S, Pintaud JC, Santoni S, Salhi-Hannachi A, Glémin S, Aberlenc-Bertossi F. Male-specific DNA markers provide genetic evidence of an XY chromosome system, a recombination arrest and allow the tracing of paternal lineages in date palm. New Phytol 2013; 197:409-415. [PMID: 23231423 DOI: 10.1111/nph.12069] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/23/2012] [Indexed: 05/26/2023]
Abstract
Whether sex chromosomes are differentiated is an important aspect of our knowledge of dioecious plants, such as date palm (Phoenix dactylifera). In this crop plant, the female individuals produce dates, and are thus the more valuable sex. However, there is no way to identify the sex of date palm plants before reproductive age, and the sex-determining mechanism is still unclear. To identify sex-linked microsatellite markers, we surveyed a set of 52 male and 55 female genotypes representing the geographical diversity of the species. We found three genetically linked loci that are heterozygous only in males. Male-specific alleles allowed us to identify the gender in 100% of individuals. These results confirm the existence of an XY chromosomal system with a nonrecombining XY-like region in the date palm genome. The distribution of Y haplotypes in western and eastern haplogroups allowed us to trace two male ancestral paternal lineages that account for all known Y diversity in date palm. The very low diversity associated with Y haplotypes is consistent with clonal paternal transmission of a nonrecombining male-determining region. Our results establish the date palm as a biological model with one of the most ancient sex chromosomes in flowering plants.
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Affiliation(s)
- Emira Cherif
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunisia
| | - Salwa Zehdi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunisia
| | - Karina Castillo
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | - Nathalie Chabrillange
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | | | | | - Sylvain Santoni
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), 34398, Montpellier, France
| | - Amel Salhi-Hannachi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092, El Manar, Tunisia
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier 2, 34095, Montpellier, France
| | - Frédérique Aberlenc-Bertossi
- IRD/CIRAD Palm Developmental Biology Group, UMR DIADE, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
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Causse M, Santoni S, Damerval C, Maurice A, Charcosset A, Deatrick J, Vienne D. A composite map of expressed sequences in maize. Genome 2012; 39:418-32. [PMID: 18469903 DOI: 10.1139/g96-053] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A maize genetic map based mainly on expressed sequences has been constructed. The map incorporates data from four segregating populations. Three recombinant inbred line populations were derived from the nonreciprocal crosses between three inbred lines. A map derived from an independent F2 progeny from one of the crosses was also used. With a total of 521 genotyped individuals, accuracy in gene order is expected. Five sources of markers were used: (i) 109 loci corresponding to 69 genes of known function, (ii) 39 loci controlling protein position shifts revealed by two-dimensional electrophoresis, (iii) 8 isozyme loci, (iv) 17 loci corresponding to 14 sequenced cDNAs for which no homology was found in gene banks, and (v) 102 loci corresponding to 81 anonymous probes. As many loci were common to all maps, we tested heterogeneity between recombination fractions. The comparison of recombination fractions revealed: (i) a good correspondence between the maps derived from the same cross, (ii) few significant differences in interval distances, and (iii) global differences, which can reach 20% of the total map length. A composite map of 275 loci covering 1765 cM has been constructed. Key words : Zea mays L., RFLP, genetic map, molecular markers, proteins.
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Bourguiba H, Audergon JM, Krichen L, Trifi-Farah N, Mamouni A, Trabelsi S, D’Onofrio C, Asma BM, Santoni S, Khadari B. Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin. BMC Plant Biol 2012; 12:49. [PMID: 22510209 PMCID: PMC3511222 DOI: 10.1186/1471-2229-12-49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 02/23/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. RESULTS According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. CONCLUSIONS A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.
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Affiliation(s)
- Hedia Bourguiba
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
- INRA Centre PACA – UR1052 GAFL, Domaine St Maurice, BP94, 84143, Montfavet Cedex, France
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Jean-Marc Audergon
- INRA Centre PACA – UR1052 GAFL, Domaine St Maurice, BP94, 84143, Montfavet Cedex, France
| | - Lamia Krichen
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Neila Trifi-Farah
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Ali Mamouni
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknès, Morocco
| | - Samia Trabelsi
- Université de Blida, Chaire d’arboriculture, Blida, Algeria
| | - Claudio D’Onofrio
- Department of Fruit Science and Plant Protection of Woody Species “G. Scaramuzzi”, section of Fruit Science, University of Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
| | - Bayram M Asma
- Department of Biology, Inonu University, Malatya, 44280, Turkey
| | - Sylvain Santoni
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
| | - Bouchaib Khadari
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
- CBNMED, UMR 1334 AGAP, F-34398, Montpellier, France
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Rousset M, Bonnin I, Remoué C, Falque M, Rhoné B, Veyrieras JB, Madur D, Murigneux A, Balfourier F, Le Gouis J, Santoni S, Goldringer I. Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theor Appl Genet 2011; 123:907-26. [PMID: 21761163 DOI: 10.1007/s00122-011-1636-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 06/13/2011] [Indexed: 05/18/2023]
Abstract
Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time. Using a collection of hexaploid wheat composed of 235 lines from diverse geographical origins, we conducted an association study for six candidate genes for flowering time and its components (vernalization sensitivity and earliness per se). The effect on the variation of earliness components of polymorphisms within the copies of each gene was tested in ANOVA models accounting for the underlying genetic structure. The collection was structured in five groups that minimized the residual covariance. Vernalization requirement and lateness tend to increase according to the mean latitude of each group. Heading date for an autumnal sowing was mainly determined by the earliness per se. Except for the Constans (CO) gene orthologous of the barley HvCO3, all gene polymorphisms had a significant impact on earliness components. The three traits used to quantify vernalization requirement were primarily associated with polymorphisms at Vrn-1 and then at Vrn-3 and Luminidependens (LD) genes. We found a good correspondence between spring/winter types and genotypes at the three homeologous copies of Vrn-1. Earliness per se was mainly explained by polymorphisms at Vrn-3 and to a lesser extent at Vrn-1, Hd-1 and Gigantea (GI) genes. Vernalization requirement and earliness as a function of geographical origin, as well as the possible role of the breeding practices in the geographical distribution of the alleles and the hypothetical adaptive value of the candidate genes, are discussed.
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Affiliation(s)
- Michel Rousset
- UMR de Génétique Végétale, INRA/CNRS/AgroParisTech/Univ. Paris XI, Ferme du Moulon, 91190 Gif sur Yvette, France.
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49
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Escobar JS, Scornavacca C, Cenci A, Guilhaumon C, Santoni S, Douzery EJP, Ranwez V, Glémin S, David J. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). BMC Evol Biol 2011; 11:181. [PMID: 21702931 PMCID: PMC3142523 DOI: 10.1186/1471-2148-11-181] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [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: 01/25/2011] [Accepted: 06/24/2011] [Indexed: 11/30/2022] Open
Abstract
Background Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of gene-tree conflicts in this tribe. Results We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-like manner. Dasypyrum, Heteranthelium and genera of clade V, grouping Secale, Taeniatherum, Triticum and Aegilops, have evolved in a reticulated manner. Their relationships are thus better represented by the multigenic network than by the supermatrix or BCF trees. Noteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. Together, our results suggest that recombination is the main factor decoupling gene trees from multigenic trees. Conclusions Our study is the first to propose a comprehensive, multigenic phylogeny of Triticeae. It clarifies several aspects of the relationships among genera and species of this tribe, and pinpoints biological groups with likely reticulate evolution. Importantly, this study extends previous results obtained in Drosophila by demonstrating that recombination can exacerbate gene-tree conflicts in phylogenetic reconstructions.
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Affiliation(s)
- Juan S Escobar
- Institut National de la Recherche Agronomique, Centre de Montpellier, UMR Diversité et Adaptation des Plantes Cultivées, Domaine de Melgueil, 34130 Mauguio, France.
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50
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Laucou V, Lacombe T, Dechesne F, Siret R, Bruno JP, Dessup M, Dessup T, Ortigosa P, Parra P, Roux C, Santoni S, Varès D, Péros JP, Boursiquot JM, This P. High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theor Appl Genet 2011; 122:1233-45. [PMID: 21234742 DOI: 10.1007/s00122-010-1527-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 12/22/2010] [Indexed: 05/20/2023]
Abstract
Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management.
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Affiliation(s)
- V Laucou
- INRA Montpellier SupAgro, UMR DIAPC, Equipe Génétique de la Vigne, Montpellier, France.
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