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Le Provost G, Lalanne C, Lesur I, Louvet JM, Delzon S, Kremer A, Labadie K, Aury JM, Da Silva C, Moritz T, Plomion C. Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. BMC PLANT BIOLOGY 2023; 23:108. [PMID: 36814198 PMCID: PMC9948485 DOI: 10.1186/s12870-023-04069-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations. RESULTS In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation. CONCLUSION Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.
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Affiliation(s)
| | | | - Isabelle Lesur
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- Helix Venture, F-33700, Mérignac, France
| | | | | | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
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Le Provost G, Brachi B, Lesur I, Lalanne C, Labadie K, Aury JM, Da Silva C, Postolache D, Leroy T, Plomion C. Gene expression and genetic divergence in oak species highlight adaptive genes to soil water constraints. PLANT PHYSIOLOGY 2022; 190:2466-2483. [PMID: 36066428 PMCID: PMC9706432 DOI: 10.1093/plphys/kiac420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Drought and waterlogging impede tree growth and may even lead to tree death. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species, pedunculate (PO; Quercus robur L.) and sessile oak (SO; Quercus petraea Matt. Lieb), have overlapping ranges, but their respective distribution are highly constrained by local soil conditions. These contrasting ecological preferences between two closely related and frequently hybridizing species constitute a powerful model to explore the functional bases of the adaptive responses in oak. We exposed oak seedlings to waterlogging and drought, conditions typically encountered by the two species in their respective habitats, and studied changes in gene expression in roots using RNA-seq. We identified genes that change in expression between treatments differentially depending on species. These "species × environment"-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with different expression between species independently of water conditions imposed. Surprisingly, this category included genes with functions consistent with a role in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the expressional candidate genes included numerous highly differentiated genetic markers between the two species. By combining transcriptomic analysis, gene annotation, pathway analyses, as well as genome scan for genetic differentiation among species, we were able to highlight loci likely involved in adaptation of the two species to their respective ecological niches.
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Affiliation(s)
| | | | - Isabelle Lesur
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, F-33610, France
- Helix Venture, Mérignac, F-33700, France
| | | | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Dragos Postolache
- National Institute for Research and Development in Forestry “Marin Drăcea”, Cluj Napoca Research Station, Cluj-Napoca, 400202, Romania
| | - Thibault Leroy
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, F-33610, France
- IRHS-UMR1345, Université d’Angers, INRAE, Institut Agro, Beaucouzé, 49071, France
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Keep Calm and Survive: Adaptation Strategies to Energy Crisis in Fruit Trees under Root Hypoxia. PLANTS 2020; 9:plants9091108. [PMID: 32867316 PMCID: PMC7570223 DOI: 10.3390/plants9091108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 01/05/2023]
Abstract
Plants are permanently facing challenges imposed by the environment which, in the context of the current scenario of global climate change, implies a constant process of adaptation to survive and even, in the case of crops, at least maintain yield. O2 deficiency at the rhizosphere level, i.e., root hypoxia, is one of the factors with the greatest impact at whole-plant level. At cellular level, this O2 deficiency provokes a disturbance in the energy metabolism which has notable consequences on the yield of plant crops. In this sense, although several physiological studies describe processes involved in plant adaptation to root hypoxia in woody fruit trees, with emphasis on the negative impacts on photosynthetic rate, there are very few studies that include -omics strategies for specifically understanding these processes in the roots of such species. Through a de novo assembly approach, a comparative transcriptome study of waterlogged Prunus spp. genotypes contrasting in their tolerance to root hypoxia was revisited in order to gain a deeper insight into the reconfiguration of pivotal pathways involved in energy metabolism. This re-analysis describes the classically altered pathways seen in the roots of woody fruit trees under hypoxia, but also routes that link them to pathways involved with nitrogen assimilation and the maintenance of cytoplasmic pH and glycolytic flow. In addition, the effects of root hypoxia on the transcription of genes related to the mitochondrial oxidative phosphorylation system, responsible for providing adenosine triphosphate (ATP) to the cell, are discussed in terms of their roles in the energy balance, reactive oxygen species (ROS) metabolism and aerenchyma formation. This review compiles key findings that help to explain the trait of tolerance to root hypoxia in woody fruit species, giving special attention to their strategies for managing the energy crisis. Finally, research challenges addressing less-explored topics in recovery and stress memory in woody fruit trees are pointed out.
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Zeng B, Zhang Y, Zhang A, Qiao D, Ren J, Li M, Cai K, Zhang J, Huang L. Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress. PHYTOCHEMISTRY 2020; 175:112378. [PMID: 32315838 DOI: 10.1016/j.phytochem.2020.112378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Submergence is one of the environmental stresses that limit plant growth and development. Dactylis glomerata L. is an important cool-season forage grass globally. To investigate the genes related to submergence response and the molecular mechanism associated with submergence tolerance, the transcriptome of D. glomerata in response to waterlogging treatment was analyzed. RNA-sequencing was performed in two D. glomerata cultivars, submergence tolerant 'Dianbei' and submergence sensitive 'Anba'. A total of 50,045 unique genes matched the known proteins in the NCBI nr database by BLAST searches and 60.8% (30,418) of these genes were annotated with GO terms. Among these, 1395 genes only differentially expressed in 'Dianbei' and 18 genes shown different expression all the time were detected between the submergence tolerant 'Dianbei' and sensitive 'Anba'. Gene ontology (GO) and KEGG pathway enrichment analyses demonstrated that the DEGs were mainly implicated in oxidation-reduction system, nucleic acid binding transcription factor activity, and glycerol kinase activity. The D. glomerata assembled transcriptome provided substantial molecular resource for further genomic analysis of forage grasses in response to submergence stress. The significant difference in expression of specific unigenes may account for waterlogging tolerance or acclimation in the two different D. glomerata cultivars. This study provided new insights into the molecular basis of submergence tolerance in D. glomerata.
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Affiliation(s)
- Bing Zeng
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Yajie Zhang
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Ailing Zhang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dandan Qiao
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Juncai Ren
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Mingyang Li
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Kai Cai
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Jinhua Zhang
- Guizhou animal Husbandry and Veterinary Institute, Guiyang, 550005, China.
| | - Linkai Huang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Menezes‐Silva PE, Loram‐Lourenço L, Alves RDFB, Sousa LF, Almeida SEDS, Farnese FS. Different ways to die in a changing world: Consequences of climate change for tree species performance and survival through an ecophysiological perspective. Ecol Evol 2019; 9:11979-11999. [PMID: 31695903 PMCID: PMC6822037 DOI: 10.1002/ece3.5663] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 01/10/2023] Open
Abstract
Anthropogenic activities such as uncontrolled deforestation and increasing greenhouse gas emissions are responsible for triggering a series of environmental imbalances that affect the Earth's complex climate dynamics. As a consequence of these changes, several climate models forecast an intensification of extreme weather events over the upcoming decades, including heat waves and increasingly severe drought and flood episodes. The occurrence of such extreme weather will prompt profound changes in several plant communities, resulting in massive forest dieback events that can trigger a massive loss of biodiversity in several biomes worldwide. Despite the gravity of the situation, our knowledge regarding how extreme weather events can undermine the performance, survival, and distribution of forest species remains very fragmented. Therefore, the present review aimed to provide a broad and integrated perspective of the main biochemical, physiological, and morpho-anatomical disorders that may compromise the performance and survival of forest species exposed to climate change factors, particularly drought, flooding, and global warming. In addition, we also discuss the controversial effects of high CO2 concentrations in enhancing plant growth and reducing the deleterious effects of some extreme climatic events. We conclude with a discussion about the possible effects that the factors associated with the climate change might have on species distribution and forest composition.
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Affiliation(s)
| | - Lucas Loram‐Lourenço
- Laboratory of Plant EcophysiologyInstituto Federal Goiano – Campus Rio VerdeGoiásBrazil
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Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin T, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Michener JK. Hardwood Tree Genomics: Unlocking Woody Plant Biology. FRONTIERS IN PLANT SCIENCE 2018; 9:1799. [PMID: 30619389 PMCID: PMC6304363 DOI: 10.3389/fpls.2018.01799] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/19/2018] [Indexed: 05/07/2023]
Abstract
Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.
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Affiliation(s)
- Gerald A. Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Andrew T. Groover
- Pacific Southwest Research Station, USDA Forest Service, Davis, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | - Alexander Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Dario Grattapaglia
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Universidade Católica de Brasília, Brasília, Brazil
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States
| | - Tongming Yin
- The Key Laboratory for Poplar Improvement of Jiangsu Province, Nanjing Forestry University, Nanjing, China
| | - Jean-Marc Aury
- Commissariat à l’Energie Atomique, Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | | | - John E. Carlson
- Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States
| | - Jennifer Randall
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jared Westbrook
- The American Chestnut Foundation, Asheville, NC, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Wellington Muchero
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Daniel Jacobson
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
| | - Joshua K. Michener
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States
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Peng Y, Zhou Z, Zhang Z, Yu X, Zhang X, Du K. Molecular and physiological responses in roots of two full-sib poplars uncover mechanisms that contribute to differences in partial submergence tolerance. Sci Rep 2018; 8:12829. [PMID: 30150759 PMCID: PMC6110812 DOI: 10.1038/s41598-018-30821-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022] Open
Abstract
Poplar is a major afforestation tree species in flood-prone areas. Here, we compared molecular and physiological responses in the roots of two full-sib poplar clones, LS1 (flood-tolerant) and LS2 (flood-susceptive), subjected to stagnant flooding using transcript and metabolite profiling. LS1 displayed less phenotypic damage and superior leaf gas exchange and plant growth compared with those of LS2. We concluded that three characteristics might contribute to the differences in flood tolerance between LS1 and LS2. First, fermentation was initiated through lactic dehydrogenation in LS1 roots under flooding and subsequently dominated by alcohol fermentation. However, lactic dehydrogenase was persistently active in flooded LS2. Second, 13 differentially expressed genes associated with energy and O2 consumption processes under soil flooding had lower transcript levels in LS1 than those in LS2, which might contribute to better energy-/O2-saving abilities and behaviours in flood-tolerant LS1 than those in flood-susceptible LS2 under hypoxic stress. Third, LS1 possessed increased reactive oxygen species scavenging abilities compared with those of LS2 under edaphic flooding. Our data are a valuable contribution to understanding the mechanisms involved in the flood tolerance of poplar.
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Affiliation(s)
- YanJie Peng
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - ZhiXiang Zhou
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhe Zhang
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - XiaoLi Yu
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - XinYe Zhang
- Hubei Academy of Forestry, Wuhan, 430075, P. R. China
| | - KeBing Du
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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Taxon-Independent and Taxon-Dependent Responses to Drought in Seedlings from Quercus robur L., Q. petraea (Matt.) Liebl. and Their Morphological Intermediates. FORESTS 2017. [DOI: 10.3390/f8110407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C, Kremer A. Extensive recent secondary contacts between four European white oak species. THE NEW PHYTOLOGIST 2017; 214:865-878. [PMID: 28085203 PMCID: PMC5624484 DOI: 10.1111/nph.14413] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Historical trajectories of tree species during the late Quaternary have been well reconstructed through genetic and palaeobotanical studies. However, many congeneric tree species are interfertile, and the timing and contribution of introgression to species divergence during their evolutionary history remains largely unknown. We quantified past and current gene flow events between four morphologically divergent oak species (Quercus petraea, Q. robur, Q. pyrenaica, Q. pubescens), by two independent inference methods: diffusion approximation to the joint frequency spectrum (∂a∂i) and approximate Bayesian computation (ABC). For each pair of species, alternative scenarios of speciation allowing gene flow over different timescales were evaluated. Analyses of 3524 single nucleotide polymorphisms (SNPs) randomly distributed in the genome, showed that these species evolved in complete isolation for most of their history, but recently came into secondary contact, probably facilitated by the most recent period of postglacial warming. We demonstrated that: there was sufficient genetic differentiation before secondary contact for the accumulation of barriers to gene flow; and current European white oak genomes are a mosaic of genes that have crossed species boundaries and genes impermeable to gene flow.
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Affiliation(s)
- Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Laure Villate
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | | | - Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jorge A P Paiva
- Instituto de Biologia Experimental e Tecnológica, iBET, Apartado 12, Oeiras, 2780-901, Portugal
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska street, Poznań, PL-60-479, Poland
| | - Carole Dossat
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | - Jean-Marc Aury
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | | | - Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
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Rellstab C, Zoller S, Walthert L, Lesur I, Pluess AR, Graf R, Bodénès C, Sperisen C, Kremer A, Gugerli F. Signatures of local adaptation in candidate genes of oaks (Quercusspp.) with respect to present and future climatic conditions. Mol Ecol 2016; 25:5907-5924. [DOI: 10.1111/mec.13889] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/22/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Christian Rellstab
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre; ETH Zürich; Universitätstrasse 16 8092 Zürich Switzerland
| | - Lorenz Walthert
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Isabelle Lesur
- UMR1202 BIOGECO; INRA; 33610 Cestas France
- UMR1202 BIOGECO; Université de Bordeaux; 33610 Talence France
- Helix Venture; 26 rue Eugène Scribe 33700 Mérignac France
| | - Andrea R. Pluess
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems; ETH Zürich; Universitätstrasse 16 8092 Zürich Switzerland
| | - René Graf
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Catherine Bodénès
- UMR1202 BIOGECO; INRA; 33610 Cestas France
- UMR1202 BIOGECO; Université de Bordeaux; 33610 Talence France
| | - Christoph Sperisen
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Antoine Kremer
- UMR1202 BIOGECO; INRA; 33610 Cestas France
- UMR1202 BIOGECO; Université de Bordeaux; 33610 Talence France
| | - Felix Gugerli
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
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Le Provost G, Lesur I, Lalanne C, Da Silva C, Labadie K, Aury JM, Leple JC, Plomion C. Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.). TREE PHYSIOLOGY 2016; 36:1330-1342. [PMID: 27358207 DOI: 10.1093/treephys/tpw056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/29/2016] [Indexed: 05/12/2023]
Abstract
Waterlogging causes stressful conditions for perennial species. The temporary overabundance of water in waterlogged soil can induce hypoxia in the rhizosphere, leading to root death, tree decline and even dieback. Two closely related members of the European white oak complex, pedunculate (Quercus robur L.) and sessile (Quercus petraea Matt. Liebl.) oaks, have different ecological characteristics, especially regarding their adaptation to soil waterlogging. The tolerance of waterlogging observed in pedunculate oak is driven principally by its ability to produce adaptive structures, hypertrophied lenticels and adventitious roots, and to switch rapidly its metabolism to the fermentative pathway. This study had two objectives: (i) to identify genes important for adaptation to waterlogging and (ii) to gain insight into the molecular mechanisms involved in hypertrophied lenticel formation in pedunculate oak. We subjected seedlings of the two species to hypoxia by maintaining the water level 2 cm above the collar. The immersed part of the stem (i.e., containing hypertrophied lenticels in pedunculate oak) was sampled after 9 days of waterlogging stress and its gene expression was investigated by RNA-seq. Genes displaying differential expression between the two species were identified with the DESeq R package and a false discovery rate of 0.001. We found that 3705 contigs were differentially regulated between the two species. Twenty-two differentially expressed genes were validated by real-time quantitative polymerase chain reaction. The suberin biosynthesis pathway was found to be upregulated in pedunculate oak, consistent with molecular mechanisms analogous to those operating in the radial oxygen loss barrier in waterlogging-tolerant species.
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Affiliation(s)
| | - Isabelle Lesur
- BIOGECO, INRA, Univ. Bordeaux, F-33610 Cestas, France
- HelixVenture, F-33700 Mérignac, France
| | | | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Jean Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Jean Charles Leple
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075 Orlèans, France
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Reeksting BJ, Olivier NA, van den Berg N. Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi. BMC PLANT BIOLOGY 2016; 16:205. [PMID: 27658453 PMCID: PMC5034587 DOI: 10.1186/s12870-016-0893-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/12/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree death. The decline of orchards infected with P. cinnamomi occurs much faster when exposed to flooding, even if flooding is only transient. Flooding is a multifactorial stress compromised of several individual stresses, making breeding and selection for tolerant varieties challenging. With more plantations occurring in marginal areas, with imperfect irrigation and drainage, understanding the response of avocado to these stresses will be important for the industry. RESULTS Maintenance of energy production was found to be central in the response to flooding, as seen by up-regulation of transcripts related to glycolysis and induction of transcripts related to ethanolic fermentation. Energy-intensive processes were generally down-regulated, as evidenced by repression of transcripts related to processes such as secondary cell-wall biosynthesis as well as defence-related transcripts. Aquaporins were found to be down-regulated in avocado roots exposed to flooding, indicating reduced water-uptake under these conditions. CONCLUSIONS The transcriptomic response of avocado to flooding and P. cinnamomi was investigated utilizing microarray analysis. Differences in the transcriptome caused by the presence of the pathogen were minor compared to transcriptomic perturbations caused by flooding. The transcriptomic response of avocado to flooding reveals a response to flooding that is conserved in several species. This data could provide key information that could be used to improve selection of stress tolerant rootstocks in the avocado industry.
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Affiliation(s)
- B. J. Reeksting
- Department of Genetics, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - N. A. Olivier
- Department of Plant Science, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - N. van den Berg
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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13
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Sloan JL, Islam MA, Jacobs DF. Reduced translocation of current photosynthate precedes changes in gas exchange for Quercus rubra seedlings under flooding stress. TREE PHYSIOLOGY 2016; 36:54-62. [PMID: 26655380 DOI: 10.1093/treephys/tpv122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/25/2015] [Indexed: 06/05/2023]
Abstract
Northern red oak (Quercus rubra L.) seedlings are frequently planted on suboptimal sites in their native range in North America, subjecting them to environmental stresses, such as flooding, for which they may not be well adapted. Members of the genus Quercus exhibit a wide range of responses to flooding, and responses of northern red oak to flooding remain inadequately described. To better understand the physiological effects of root system inundation in post-transplant northern red oak seedlings and the effects of flooding on endogenous patterns of resource allocation within the plant, we observed the effects of short-term flooding initiated at the linear shoot growth stage on net photosynthetic rates, dark respiration, chlorophyll fluorescence (Fv/Fm) and translocation of (13)C-labeled current photosynthate. Downward translocation of current photosynthate declined after 4 days of flooding and was the first measured physiological response to flooding; net photosynthetic rates decreased and dark respiration rates increased after 7 days of flooding. Short-term flooding did not affect maximal potential efficiency of photosystem II (Fv/Fm). The finding that decreased downward translocation of (13)C-labeled current photosynthate preceded reduced net photosynthesis and increased dark respiration during flooding suggests the occurrence of sink-limited photosynthesis under these conditions.
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Affiliation(s)
- Joshua L Sloan
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47901-2061, USA Present address: John T. Harrington Forestry Research Center, New Mexico State University, PO Box 359, Mora, NM 87732, USA
| | - M Anisul Islam
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47901-2061, USA Present address: Kuwait Institute for Scientific Research, PO Box 24885, Safat 13109, Kuwait
| | - Douglass F Jacobs
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47901-2061, USA
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14
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Rasheed-Depardieu C, Parelle J, Tatin-Froux F, Parent C, Capelli N. Short-term response to waterlogging in Quercus petraea and Quercus robur: A study of the root hydraulic responses and the transcriptional pattern of aquaporins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:323-30. [PMID: 26519820 DOI: 10.1016/j.plaphy.2015.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 05/02/2023]
Abstract
We characterized the short-term response to waterlogging in Quercus petraea (Matt.) Liebl. and Quercus robur L. as the initial response towards their known long-term differences in tolerance to waterlogging. One-month old seedlings were subjected to hypoxic stress and leaf gas exchange, shoot water potential (Ψs) and root hydraulic conductivity (Lpr) were measured. In parallel, the expression of nine aquaporins (AQPs) along the primary root was analysed by quantitative RT-PCR. Results showed a similar reduction in net assimilation (A) and stomatal conductance (gs) for the two species. Notably, the response of Lpr differed temporally between the two species. Q. robur seedlings exhibited a significant early decline of Lpr within the first 5 h that returned to control levels after 48 h, whereas Q. petraea seedlings showed a delayed response with a significant decrease of Lpr exhibited only after 48 h. Transcriptional profiling revealed that three genes (PIP1;3, TIP2;1 and TIP2;2) were differentially regulated under stress conditions in the two oak species. Taken together, these results suggested species-specific responses to short-term waterlogging in terms of root water transport.
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Affiliation(s)
- Claire Rasheed-Depardieu
- UMR 6249 Chrono-Environnement, Usc INRA, CNRS - Université de Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France.
| | - Julien Parelle
- UMR 6249 Chrono-Environnement, Usc INRA, CNRS - Université de Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Fabienne Tatin-Froux
- UMR 6249 Chrono-Environnement, Usc INRA, CNRS - Université de Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Claire Parent
- UMR 6249 Chrono-Environnement, Usc INRA, CNRS - Université de Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Nicolas Capelli
- UMR 6249 Chrono-Environnement, Usc INRA, CNRS - Université de Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France.
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15
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Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 2015; 16:254-65. [PMID: 25944057 DOI: 10.1111/1755-0998.12425] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022]
Abstract
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
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Affiliation(s)
- Christophe Plomion
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Joëlle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Tina Alaeitabar
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Catherine Bodénès
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Christophe Boury
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Sébastien Duplessis
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Barbara Estrada-Mairey
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Stéphanie Fouteau
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | | | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans, F-45075, France
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Thibault Leroy
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Isabelle Lesur
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Francis Martin
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Célia Michotey
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Franck Salin
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Delphine Steinbach
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | | | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.,Université d'Evry Val d'Essone, UMR 8030, Evry, CP5706, France.,Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, CP5706, France
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
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16
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Lepoittevin C, Bodénès C, Chancerel E, Villate L, Lang T, Lesur I, Boury C, Ehrenmann F, Zelenica D, Boland A, Besse C, Garnier-Géré P, Plomion C, Kremer A. Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks. Mol Ecol Resour 2015; 15:1446-59. [DOI: 10.1111/1755-0998.12407] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- C. Lepoittevin
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - C. Bodénès
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - E. Chancerel
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - L. Villate
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - T. Lang
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla Yunnan 666303 China
| | - I. Lesur
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
- HelixVenture; Mérignac F-33700 France
| | - C. Boury
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - F. Ehrenmann
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - D. Zelenica
- CEA, Institut de Génomique, Centre National de Génotypage; 2 rue Gaston Crémieux, CP5721 Evry Cedex F-91057 France
| | - A. Boland
- CEA, Institut de Génomique, Centre National de Génotypage; 2 rue Gaston Crémieux, CP5721 Evry Cedex F-91057 France
| | - C. Besse
- CEA, Institut de Génomique, Centre National de Génotypage; 2 rue Gaston Crémieux, CP5721 Evry Cedex F-91057 France
| | - P. Garnier-Géré
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - C. Plomion
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
| | - A. Kremer
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33600 France
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17
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Lesur I, Bechade A, Lalanne C, Klopp C, Noirot C, Leplé JC, Kremer A, Plomion C, Le Provost G. A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Mol Ecol Resour 2015; 15:1192-204. [PMID: 25594128 DOI: 10.1111/1755-0998.12373] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/06/2015] [Accepted: 01/13/2015] [Indexed: 11/27/2022]
Abstract
Systematic sequencing is the method of choice for generating genomic resources for molecular marker development and candidate gene identification in nonmodel species. We generated 47,357 Sanger ESTs and 2.2M Roche-454 reads from five cDNA libraries for European beech (Fagus sylvatica L.). This tree species of high ecological and economic value in Europe is among the most representative trees of deciduous broadleaf forests. The sequences generated were assembled into 21,057 contigs with MIRA software. Functional annotations were obtained for 85% of these contigs, from the proteomes of four plant species, Swissprot accessions and the Gene Ontology database. We were able to identify 28,079 in silico SNPs for future marker development. Moreover, RNAseq and qPCR approaches identified genes and gene networks regulated differentially between two critical phenological stages preceding vegetative bud burst (the quiescent and swelling buds stages). According to climatic model-based projection, some European beech populations may be endangered, particularly at the southern and eastern edges of the European distribution range, which are strongly affected by current climate change. This first genomic resource for the genus Fagus should facilitate the identification of key genes for beech adaptation and management strategies for preserving beech adaptability.
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Affiliation(s)
- Isabelle Lesur
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.,Helix Venture, F-33700, Mérignac, France
| | - Alison Bechade
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France
| | - Christophe Klopp
- Plateforme bioinformatique Genotoul, UR875UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France
| | - Céline Noirot
- Plateforme bioinformatique Genotoul, UR875UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France
| | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France
| | - Christophe Plomion
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.,Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France
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18
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A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks. Heredity (Edinb) 2014; 114:373-86. [PMID: 25515016 DOI: 10.1038/hdy.2014.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/11/2014] [Accepted: 11/12/2014] [Indexed: 01/09/2023] Open
Abstract
We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the 'species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory.
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19
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Kreuzwieser J, Rennenberg H. Molecular and physiological responses of trees to waterlogging stress. PLANT, CELL & ENVIRONMENT 2014; 37:2245-59. [PMID: 24611781 DOI: 10.1111/pce.12310] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/09/2014] [Accepted: 02/12/2014] [Indexed: 05/23/2023]
Abstract
One major effect of global climate change will be altered precipitation patterns in many regions of the world. This will cause a higher probability of long-term waterlogging in winter/spring and flash floods in summer because of extreme rainfall events. Particularly, trees not adapted at their natural site to such waterlogging stress can be impaired. Despite the enormous economic, ecological and social importance of forest ecosystems, the effect of waterlogging on trees is far less understood than the effect on many crops or the model plant Arabidopsis. There is only a handful of studies available investigating the transcriptome and metabolome of waterlogged trees. Main physiological responses of trees to waterlogging include the stimulation of fermentative pathways and an accelerated glycolytic flux. Many energy-consuming, anabolic processes are slowed down to overcome the energy crisis mediated by waterlogging. A crucial feature of waterlogging tolerance is the steady supply of glycolysis with carbohydrates, particularly in the roots; stress-sensitive trees fail to maintain sufficient carbohydrate availability resulting in the dieback of the stressed tissues. The present review summarizes physiological and molecular features of waterlogging tolerance of trees; the focus is on carbon metabolism in both, leaves and roots of trees.
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Affiliation(s)
- Jürgen Kreuzwieser
- Institute of Forest Science, Chair of Tree Physiology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79110, Germany
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20
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Lagache L, Klein EK, Ducousso A, Petit RJ. Distinct male reproductive strategies in two closely related oak species. Mol Ecol 2014; 23:4331-43. [DOI: 10.1111/mec.12766] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/12/2014] [Accepted: 04/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Lélia Lagache
- INRA; UMR 1202 Biogeco; F-33610 Cestas France
- Univ. Bordeaux; UMR1202 Biogeco; F-33400 Talence France
| | - Etienne K. Klein
- Biostatistique et Processus Spatiaux (BioSP); INRA; UR546; F-84914 Avignon France
| | - Alexis Ducousso
- INRA; UMR 1202 Biogeco; F-33610 Cestas France
- Univ. Bordeaux; UMR1202 Biogeco; F-33400 Talence France
| | - Rémy J. Petit
- INRA; UMR 1202 Biogeco; F-33610 Cestas France
- Univ. Bordeaux; UMR1202 Biogeco; F-33400 Talence France
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21
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Kogawara S, Yamanoshita T, Norisada M, Kojima K. Steady sucrose degradation is a prerequisite for tolerance to root hypoxia. TREE PHYSIOLOGY 2014; 34:229-40. [PMID: 24646690 DOI: 10.1093/treephys/tpu013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We investigated the role of glycolysis and sucrolysis in the difference in tolerance to root hypoxia between two Myrtaceae tree species, Melaleuca cajuputi (which shows superior tolerance to root hypoxia) and Eucalyptus camaldulensis (which does not). Analysis of the adenylate energy charge (AEC) in roots subjected to a 4-day hypoxic treatment (HT) in hydroponic culture revealed that the interspecies difference in tolerance corresponds to the ability to maintain energy status under root hypoxia: AEC was reduced by HT in E. camaldulensis, but not in M. cajuputi. The energy status in HT roots of E. camaldulensis was restored by feeding of glucose (Glc) but not sucrose (Suc). These data provide evidence that low substrate availability for glycolysis resulting from an impairment of sucrolysis suppresses ATP production under hypoxic conditions in this species. Measurements of the rates of O2 consumption and CO2 production in roots indicated that E. camaldulensis, but not M. cajuputi, failed to activate fermentation in HT roots. These results cannot be attributed to enzymatic dysfunction, because no inhibition of main glycolytic and fermentative enzymes was observed in both species, and Glc feeding had a beneficial effect on AEC of HT roots of E. camaldulensis. The impairment of sucrolysis was demonstrated by inhibited soluble acid invertase activity in HT roots of E. camaldulensis. In contrast, there was no inhibition in all sucrolytic enzymes tested in HT roots of M. cajuputi, suggesting that steady Suc degradation is essential for maintaining high energy status under root hypoxia. We conclude that root sucrolysis is one of the essential factors that determines the extent of tolerance to root hypoxia.
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Affiliation(s)
- Satoshi Kogawara
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo 113-8657, Japan
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Lee YH, Kim KS, Jang YS, Hwang JH, Lee DH, Choi IH. Global gene expression responses to waterlogging in leaves of rape seedlings. PLANT CELL REPORTS 2014; 33:289-299. [PMID: 24384821 DOI: 10.1007/s00299-013-1529-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 06/03/2023]
Abstract
Soil waterlogging is a serious constraint to crop production. We investigated the physiological responses of rape (Brassica napus L.) seedlings to waterlogging stress and analyzed global gene transcription responses in the aerial leaves of waterlogged rape seedlings. Seedlings of 'Tammi' and 'Youngsan' cultivars were subjected to waterlogging for 3 and 6 days and recovery for 5 days. Waterlogging stress caused a significant decrease in leaf chlorophyll content and premature senescence of the leaves. Maximal quantum efficiency of PSII (F(v)/F(m)) decreased in the waterlogged seedlings compared with the control plants. To evaluate whether the observed physiological changes in the leaves are associated with the differential regulation of gene expression in response to waterlogging stress, we analyzed the global transcriptional profile of leaves of 'Tammi' seedlings that were exposed to waterlogging for a short period (36 and 72 h). SolexaQA RNA-seq analysis revealed that a total of 4,484 contigs (8.5 %) of all contigs assayed (52,747) showed a twofold change in expression after 36 h of the start of waterlogging and 9,659 contigs (18.3 %) showed a twofold change after 72 h. Major genes involved in leaf photosynthesis, including light reactions and carbon-fixing reactions, were downregulated, while a number of genes involved in the scavenging of reactive oxygen species, degradation (proteins, starch, and lipids), premature senescence, and abiotic stress tolerance were upregulated. Transcriptome analysis data suggested that the aerial leaves of waterlogged rape seedlings respond to hypoxia by regulating the expression of diverse genes in the leaves.
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Affiliation(s)
- Yong-Hwa Lee
- Bioenergy Crop Research Center, National Institute of Crop Science, Rural Development Administration, Muan, 533-834, Republic of Korea,
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Le Provost G, Domergue F, Lalanne C, Ramos Campos P, Grosbois A, Bert D, Meredieu C, Danjon F, Plomion C, Gion JM. Soil water stress affects both cuticular wax content and cuticle-related gene expression in young saplings of maritime pine (Pinus pinaster Ait). BMC PLANT BIOLOGY 2013; 13:95. [PMID: 23815794 PMCID: PMC3728238 DOI: 10.1186/1471-2229-13-95] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 06/28/2013] [Indexed: 05/25/2023]
Abstract
BACKGROUND The cuticle is a hydrophobic barrier located at the aerial surface of all terrestrial plants. Recent studies performed on model plants, such as Arabidopsis thaliana, have suggested that the cuticle may be involved in drought stress adaptation, preventing non-stomatal water loss. Although forest trees will face more intense drought stresses (in duration and intensity) with global warming, very few studies on the role of the cuticle in drought stress adaptation in these long-lived organisms have been so far reported. RESULTS This aspect was investigated in a conifer, maritime pine (Pinus pinaster Ait.), in a factorial design with two genetic units (two half-sib families with different growth rates) and two treatments (irrigated vs non-irrigated), in field conditions. Saplings were grown in an open-sided greenhouse and half were irrigated three times per week for two growing seasons. Needles were sampled three times per year for cuticular wax (composition and content) and transcriptome (of 11 genes involved in cuticle biosynthesis) analysis. Non-irrigated saplings (i) had a higher cuticular wax content than irrigated saplings and (ii) overexpressed most of the genes studied. Both these trends were more marked in the faster growing family. CONCLUSIONS The higher cuticular wax content observed in the non-irrigated treatment associated with strong modifications in products from the decarbonylation pathway suggest that cuticular wax may be involved in drought stress adaptation in maritime pine. This study provides also a set of promising candidate genes for future forward genetic studies in conifers.
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Affiliation(s)
- Grégoire Le Provost
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Frédéric Domergue
- Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, UMR5200, F-33000, Bordeaux, France
- CNRS, Laboratoire de Biogenèse Membranaire, UMR5200, F-33000, Bordeaux, France
| | - Céline Lalanne
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Patricio Ramos Campos
- Instituto Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Antoine Grosbois
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Didier Bert
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Céline Meredieu
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Frédéric Danjon
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Christophe Plomion
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
| | - Jean-Marc Gion
- INRA, UMR 1202, BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, BIOGECO, UMR 1202, F-33400, Talence, France
- CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398, Montpellier Cedex 5, France
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24
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Rasheed-Depardieu C, Parent C, Crèvecoeur M, Parelle J, Tatin-Froux F, Le Provost G, Capelli N. Identification and expression of nine oak aquaporin genes in the primary root axis of two oak species, Quercus petraea and Quercus robur. PLoS One 2012; 7:e51838. [PMID: 23284785 PMCID: PMC3524086 DOI: 10.1371/journal.pone.0051838] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 11/07/2012] [Indexed: 12/01/2022] Open
Abstract
Aquaporins (AQPs) belong to the Major Intrinsic Protein family that conducts water and other small solutes across biological membranes. This study aimed to identify and characterize AQP genes in the primary root axis of two oak species, Quercus petraea and Quercus robur. Nine putative AQP genes were cloned, and their expression was profiled in different developmental root zones by real-time PCR. A detailed examination of the predicted amino acid sequences and subsequent phylogenetic analysis showed that the isolated AQPs could be divided into two subfamilies, which included six plasma membrane intrinsic proteins (PIPs) and three tonoplast intrinsic proteins (TIPs). We characterized the anatomical features of the roots and defined three developmental root zones: the immature, transition and mature zones. Expression analysis of the AQPs was performed according to these root developmental stages. Our results showed that the expression of PIP2;3 and TIP1 was significantly higher in Quercus petraea compared with Quercus robur in the three root zones. However, PIP2;1 and TIP2;1 were found to be differentially expressed in the mature zone of the two oak species. Of the nine AQP genes identified and analyzed, we highlighted four genes that might facilitate a deeper understanding of how these two closely related tree species adapted to different environments.
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Affiliation(s)
| | - Claire Parent
- Université de Franche-Comté, UMR 6249 Chrono-Environnement, Besançon, France
| | - Michèle Crèvecoeur
- Département de Botanique et Biologie végétale, Université de Genève, Genève, Suisse
| | - Julien Parelle
- Université de Franche-Comté, UMR 6249 Chrono-Environnement, Besançon, France
| | | | - Grégoire Le Provost
- UMR 1202 BIOGECO, INRA, Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, Talence, France
| | - Nicolas Capelli
- Université de Franche-Comté, UMR 6249 Chrono-Environnement, Besançon, France
- * E-mail:
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Lagache L, Klein EK, Guichoux E, Petit RJ. Fine-scale environmental control of hybridization in oaks. Mol Ecol 2012; 22:423-36. [PMID: 23173566 DOI: 10.1111/mec.12121] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/31/2012] [Accepted: 09/11/2012] [Indexed: 12/14/2022]
Abstract
Natural hybridization is attracting much interest in modern speciation and conservation biology studies, but the underlying mechanisms remain poorly understood. In particular, it is unclear why environmental changes often increase hybridization rates. To study this question, we surveyed mating events in a mixed oak stand and developed a spatially explicit individual-based hybridization model. This model, where hybridization is frequency-dependent, pollen is nonlimiting and which allows immigrant pollen to compete with local pollen, takes into account species-specific pollen dispersal and sexual barriers to hybridization. The consequences of pollen limitation on hybridization were studied using another simple model. The results indicate that environmental changes could increase hybridization rates through two distinct mechanisms. First, by disrupting the spatial organization of communities, they should decrease the proportion of conspecific pollen available for mating, thus increasing hybridization rates. Second, by decreasing the density of conspecifics, they should increase pollen limitation and thus hybridization rates, as a consequence of chance pollination predominating over deterministic pollen competition. Altogether, our results point to a need for considering hybridization events at the appropriate level of organization and provide new insights into why hybridization rates generally increase in disturbed environments.
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Affiliation(s)
- Lélia Lagache
- INRA, UMR1202 Biogeco, F- 33610, Cestas, France; UMR1202 Biogeco, Univ. Bordeaux, F-33400, Talence, France
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