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Neugart S, Steininger V, Fernandes C, Martínez-Abaigar J, Núñez-Olivera E, Schreiner M, Strid Å, Viczián A, Albert A, Badenes-Pérez FR, Castagna A, Dáder B, Fereres A, Gaberscik A, Gulyás Á, Gwynn-Jones D, Nagy F, Jones A, Julkunen-Tiitto R, Konstantinova N, Lakkala K, Llorens L, Martínez-Lüscher J, Nybakken L, Olsen J, Pascual I, Ranieri A, Regier N, Robson M, Rosenqvist E, Santin M, Turunen M, Vandenbussche F, Verdaguer D, Winkler B, Witzel K, Grifoni D, Zipoli G, Hideg É, Jansen MAK, Hauser MT. A synchronized, large-scale field experiment using Arabidopsis thaliana reveals the significance of the UV-B photoreceptor UVR8 under natural conditions. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38881245 DOI: 10.1111/pce.15008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
This study determines the functional role of the plant ultraviolet-B radiation (UV-B) photoreceptor, UV RESISTANCE LOCUS 8 (UVR8) under natural conditions using a large-scale 'synchronized-genetic-perturbation-field-experiment'. Laboratory experiments have demonstrated a role for UVR8 in UV-B responses but do not reflect the complexity of outdoor conditions where 'genotype × environment' interactions can mask laboratory-observed responses. Arabidopsis thaliana knockout mutant, uvr8-7, and the corresponding Wassilewskija wild type, were sown outdoors on the same date at 21 locations across Europe, ranging from 39°N to 67°N latitude. Growth and climatic data were monitored until bolting. At the onset of bolting, rosette size, dry weight, and phenolics and glucosinolates were quantified. The uvr8-7 mutant developed a larger rosette and contained less kaempferol glycosides, quercetin glycosides and hydroxycinnamic acid derivatives than the wild type across all locations, demonstrating a role for UVR8 under field conditions. UV effects on rosette size and kaempferol glycoside content were UVR8 dependent, but independent of latitude. In contrast, differences between wild type and uvr8-7 in total quercetin glycosides, and the quercetin-to-kaempferol ratio decreased with increasing latitude, that is, a more variable UV response. Thus, the large-scale synchronized approach applied demonstrates a location-dependent functional role of UVR8 under natural conditions.
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Affiliation(s)
- Susanne Neugart
- Division Quality and Sensory of Plant Products, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Viktoria Steininger
- Department of Applied Genetics & Cell Biology, University of Natural Resources & Life Sciences, Vienna, Austria
| | - Catarina Fernandes
- Department of Applied Genetics & Cell Biology, University of Natural Resources & Life Sciences, Vienna, Austria
| | | | | | - Monika Schreiner
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Åke Strid
- Department of Natural Sciences, School of Science and Technology, Örebro University, Örebro, Sweden
| | - András Viczián
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Andreas Albert
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Antonella Castagna
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Beatriz Dáder
- Department of Agricultural Production, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - Alberto Fereres
- Institute of Agricultural Sciences, Spanish Council for Scientific Research, Madrid, Spain
| | - Alenka Gaberscik
- Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Ágnes Gulyás
- Department of Climatology and Landscape Ecology, University of Szeged, Szeged, Hungary
| | - Dylan Gwynn-Jones
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ferenc Nagy
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Alan Jones
- Earthwatch Europe, Oxford, UK
- Scion, New Zealand Forest Research Institute, Rotorua, New Zealand
| | | | - Nataliia Konstantinova
- Department of Applied Genetics & Cell Biology, University of Natural Resources & Life Sciences, Vienna, Austria
| | - Kaisa Lakkala
- Finnish Meteorological Institute - Space and Earth Observation Centre, Sodankylä, Finland
| | - Laura Llorens
- Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Johann Martínez-Lüscher
- Plant Stress Physiology group (Associated Unit to EEAD, CSIC), BIOMA Institute for Biodiversity and the Environment, University of Navarra, Pamplona, Spain
| | - Line Nybakken
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Jorunn Olsen
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Inmaculada Pascual
- Plant Stress Physiology group (Associated Unit to EEAD, CSIC), BIOMA Institute for Biodiversity and the Environment, University of Navarra, Pamplona, Spain
| | - Annamaria Ranieri
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Nicole Regier
- Earth and Environment Sciences, Forel Institute, Geneva University, Geneva, Switzerland
| | - Matthew Robson
- Organismal & Evolutionary Biology (OEB), Viikki Plant Science Centre (ViPS), Faculty of Biological & Environmental Sciences, University of Helsinki, Helsinki, Finland
- National School of Forestry, University of Cumbria, Ambleside, UK
| | - Eva Rosenqvist
- Institute of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Tåstrup, Denmark
| | - Marco Santin
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Minna Turunen
- Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Dolors Verdaguer
- Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Daniele Grifoni
- National Research Council, Institute of Bioeconomy, Sesto Fiorentino, Italy
- Laboratory of Monitoring and Environmental Modelling for the Sustainable Development (LaMMA Consortium), Sesto Fiorentino, Italy
| | - Gaetano Zipoli
- National Research Council Institute for Biometeorology, Sesto Fiorentino, Italy
| | - Éva Hideg
- Department of Plant Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Marcel A K Jansen
- Environmental Research Institute, School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland
| | - Marie-Theres Hauser
- Department of Applied Genetics & Cell Biology, University of Natural Resources & Life Sciences, Vienna, Austria
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2
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Oakley CG, Schemske DW, McKay JK, Ågren J. Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment. Mol Ecol 2023; 32:4570-4583. [PMID: 37317048 DOI: 10.1111/mec.17045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.
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Affiliation(s)
- Christopher G Oakley
- Department of Botany and Plant Pathology, and the Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan, USA
| | - John K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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3
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Baumgarten L, Pieper B, Song B, Mane S, Lempe J, Lamb J, Cooke EL, Srivastava R, Strütt S, Žanko D, Casimiro PGP, Hallab A, Cartolano M, Tattersall AD, Huettel B, Filatov DA, Pavlidis P, Neuffer B, Bazakos C, Schaefer H, Mott R, Gan X, Alonso-Blanco C, Laurent S, Tsiantis M. Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns. PLoS Biol 2023; 21:e3002191. [PMID: 37463141 PMCID: PMC10353826 DOI: 10.1371/journal.pbio.3002191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/10/2023] [Indexed: 07/20/2023] Open
Abstract
We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.
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Affiliation(s)
- Lukas Baumgarten
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bjorn Pieper
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sébastien Mane
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Janne Lempe
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonathan Lamb
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Elizabeth L. Cooke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rachita Srivastava
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Stefan Strütt
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Danijela Žanko
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Asis Hallab
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maria Cartolano
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Crete, Greece
| | - Barbara Neuffer
- Department of Botany, University of Osnabrück, Osnabrück, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hanno Schaefer
- Department Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Richard Mott
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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4
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Novikova PY, Kolesnikova UK, Scott AD. Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. PLANT REPRODUCTION 2023; 36:125-138. [PMID: 36282331 PMCID: PMC9957919 DOI: 10.1007/s00497-022-00451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 05/15/2023]
Abstract
Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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Affiliation(s)
- Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.
| | - Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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5
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N'Diaye A, Tonessia DC, Le Cunff L, Hamon P, Hamon S. RETRACTED ARTICLE: Evidence of weak genetic differentiation of Striga gesnerioides populations collected in Senegal: possible relationship with traditional cowpea seed management. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1. [PMID: 19484430 DOI: 10.1007/s00122-009-1073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 05/13/2009] [Indexed: 05/27/2023]
Affiliation(s)
- Amidou N'Diaye
- INRA, UMR DIAPC, 2 Place Pierre Viala, 34060, Montpellier Cedex 01, France.
| | | | - Loïc Le Cunff
- INRA, UMR DIAPC, 2 Place Pierre Viala, 34060, Montpellier Cedex 01, France
| | - Perla Hamon
- IRD, UMR DIAPC, 911 Av Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Serge Hamon
- IRD, UMR DIAPC, 911 Av Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
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6
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Kornstad T, Ohlson M, Fjellheim S. Phenotypic responses to light, water, and nutrient conditions in the allopolyploid
Arabidopsis suecica
and its parent species
A. thaliana
and
A. arenosa
: Does the allopolyploid outrange its parents? Ecol Evol 2022; 12:e8915. [PMID: 35592071 PMCID: PMC9101594 DOI: 10.1002/ece3.8915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/18/2022] [Accepted: 04/14/2022] [Indexed: 11/26/2022] Open
Abstract
Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor, and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid Arabidopsis suecica and its parent species A. arenosa and A. thaliana were chosen as a model system to investigate relationships between phenotypic plasticity, fitness, and genetic variation. Particularly, we test if A. suecica is more plastic, show higher genetic diversity, and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water, and light, while genetic diversity was assessed through analysis of AFLP markers. Arabidopsis arenosa showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity was found in the inbreeding A. thaliana. Geographic spacing of populations might explain the clear genetic structure in A. arenosa, while the lack of structure in A. suecica could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed toward A. arenosa having lower fitness under poor environmental conditions. Arabidopsis suecica, on the other hand, showed tendencies toward keeping up fitness under different environmental conditions.
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Affiliation(s)
| | - Mikael Ohlson
- Faculty of environmental sciences and natural resource management Norwegian University of Life Sciences Ås Norway
| | - Siri Fjellheim
- Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
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7
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Cucina A, Cunsolo V, Di Francesco A, Saletti R, Zilberstein G, Zilberstein S, Tikhonov A, Bublichenko AG, Righetti PG, Foti S. Meta-proteomic analysis of the Shandrin mammoth by EVA technology and high-resolution mass spectrometry: what is its gut microbiota telling us? Amino Acids 2021; 53:1507-1521. [PMID: 34453585 PMCID: PMC8519927 DOI: 10.1007/s00726-021-03061-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022]
Abstract
During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .
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Affiliation(s)
- Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | | | | | - Alexei Tikhonov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Andrey G Bublichenko
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering ''Giulio Natta'', Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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8
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Eyer PA, Blumenfeld AJ, Johnson LNL, Perdereau E, Shults P, Wang S, Dedeine F, Dupont S, Bagnères AG, Vargo EL. Extensive human-mediated jump dispersal within and across the native and introduced ranges of the invasive termite Reticulitermes flavipes. Mol Ecol 2021; 30:3948-3964. [PMID: 34142394 DOI: 10.1111/mec.16022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 06/03/2021] [Accepted: 06/14/2021] [Indexed: 12/29/2022]
Abstract
As native ranges are often geographically structured, invasive species originating from a single source population only carry a fraction of the genetic diversity present in their native range. The invasion process is thus often associated with a drastic loss of genetic diversity resulting from a founder event. However, the fraction of diversity brought to the invasive range may vary under different invasion histories, increasing with the size of the propagule, the number of reintroduction events, and/or the total genetic diversity represented by the various source populations in a multiple-introduction scenario. In this study, we generated a SNP data set for the invasive termite Reticulitermes flavipes from 23 native populations in the eastern United States and six introduced populations throughout the world. Using population genetic analyses and approximate Bayesian computation random forest, we investigated its worldwide invasion history. We found a complex invasion pathway with multiple events out of the native range and bridgehead introductions from the introduced population in France. Our data suggest that extensive long-distance jump dispersal appears common in both the native and introduced ranges of this species, probably through human transportation. Overall, our results show that similar to multiple introduction events into the invasive range, admixture in the native range prior to invasion can potentially favour invasion success by increasing the genetic diversity that is later transferred to the introduced range.
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Affiliation(s)
- Pierre-André Eyer
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, USA
| | | | - Laura N L Johnson
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, USA.,Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | | | - Phillip Shults
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, USA
| | - Shichen Wang
- Texas A&M Agrilife Genomics and Bioinformatics Service, College Station, TX, USA
| | | | - Simon Dupont
- IRBI, UMR 7261 CNRS-Université de Tours, Tours, France
| | - Anne-Geneviève Bagnères
- IRBI, UMR 7261 CNRS-Université de Tours, Tours, France.,CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, Montpellier, France
| | - Edward L Vargo
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, USA
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9
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De Kort H, Panis B, Deforce D, Van Nieuwerburgh F, Honnay O. Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales. Mol Ecol 2020; 29:4871-4881. [DOI: 10.1111/mec.15689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology University of Leuven Leuven Belgium
| | - Bart Panis
- Bioversity InternationalK.U. Leuven Leuven Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology Ghent University Ghent Belgium
| | | | - Ollivier Honnay
- Plant Conservation and Population Biology University of Leuven Leuven Belgium
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10
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Castilla AR, Méndez-Vigo B, Marcer A, Martínez-Minaya J, Conesa D, Picó FX, Alonso-Blanco C. Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evol Biol 2020; 20:71. [PMID: 32571210 PMCID: PMC7310121 DOI: 10.1186/s12862-020-01635-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation-isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)-in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. RESULTS IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana. In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana. CONCLUSIONS Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana.
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Affiliation(s)
- Antonio R Castilla
- Centre for Applied Ecology "Prof. Baeta Neves", InBIO, School of Agriculture, University of Lisbon, Lisbon, Portugal
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Centre de Recerca Ecològica i Aplicacions Forestals, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
| | | | - David Conesa
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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11
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Alvarez M, Bleich A, Donohue K. Genotypic variation in the persistence of transgenerational responses to seasonal cues. Evolution 2020; 74:2265-2280. [PMID: 32383475 DOI: 10.1111/evo.13996] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 01/01/2023]
Abstract
Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct components, or even whether they exhibit genetic variation. We tested for genetic differences in the inducibility, temporal persistence, and environmental stability of transgenerational environmental effects in Arabidopsis thaliana. Genetic variation existed in the inducibility of transgenerational effects on traits expressed across the life cycle. Surprisingly, the persistence of transgenerational effects into the third generation was uncorrelated with their induction in the second generation. Although environmental effects for some traits in some genotypes weakened over successive generations, others were stronger or even in the opposite direction in more distant generations. Therefore, transgenerational effects in more distant generations are not merely caused by the retention or dissipation of those expressed in prior generations, but they may be genetically independent traits with the potential to evolve independently.
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Affiliation(s)
- Mariano Alvarez
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - Andrew Bleich
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - Kathleen Donohue
- Department of Biology, Duke University, Durham, North Carolina, 27708
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12
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Sanderson BJ, Park S, Jameel MI, Kraft JC, Thomashow MF, Schemske DW, Oakley CG. Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual. AMERICAN JOURNAL OF BOTANY 2020; 107:250-261. [PMID: 31762012 PMCID: PMC7065183 DOI: 10.1002/ajb2.1385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress. METHODS We examined the consequences of a naturally occurring loss-of-function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing-tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. RESULTS Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. CONCLUSIONS We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold-acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.
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Affiliation(s)
- Brian J. Sanderson
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Sunchung Park
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
- Present address:
USDA ARS SalinasCAUSA
| | - M. Inam Jameel
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Present address:
Department of GeneticsUniversity of GeorgiaAthensGAUSA
| | - Joshua C. Kraft
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Michael F. Thomashow
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
| | - Douglas W. Schemske
- Department of Plant Biology, and W. K. Kellogg Biological StationMichigan State UniversityEast LansingMIUSA
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
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Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:2526-2534. [PMID: 31964817 PMCID: PMC7007534 DOI: 10.1073/pnas.1912451117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The seasonal timing of seed germination is critical for plant fitness in different climates. To germinate at the right time of year, seeds respond to seasonal environmental cues, such as cold temperatures. We characterized genetic variation in seed dormancy responses to cold across the geographic range of a widespread annual plant. Induction of secondary seed dormancy during winter conditions (which restricts germination to autumn) was positively correlated with flowering time, constructing winter and spring seasonal life-history strategies. Variation in seed chilling responses was strongly associated with functional variants of a known dormancy gene. These variants showed evidence of ancient diversification associated with Pleistocene glacial cycles, and were associated with climate gradients across the species’ geographical range. The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.
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Mattila TM, Laenen B, Slotte T. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems. Methods Mol Biol 2020; 2090:269-287. [PMID: 31975171 DOI: 10.1007/978-1-0716-0199-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
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Genetic Diversity of Field Pennycress (Thlaspi arvense) Reveals Untapped Variability and Paths Toward Selection for Domestication. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9060302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Evaluation of genetic diversity within wild populations is an essential process for improvement and domestication of new crop species. This process involves evaluation of population structure and individual accessions based on genetic markers, growth habits, and geographic collection area. In this study, accessions of field pennycress were analyzed to identify population structure and variation in germplasm available for breeding. A total of 9157 genome-wide single nucleotide polymorphisms (SNPs) were identified among the 121 accessions analyzed, and linkage disequilibrium based pruning resulted in 3497 SNPs. Bayesian cluster analysis was implemented in STRUCTURE v2.3.4 to identify four population groups. These groups were confirmed based on principal components analysis and geographic origins. Pairwise diversity among accessions was evaluated and revealed considerable genetic variation. Notably, a subset of accessions from Armenia with exceptional genetic variation was identified. This survey is the first to report significant genetic diversity among pennycress accessions and explain some of the phenotypic differences previously observed in the germplasm. Understanding variation in pennycress accessions will be a crucial step for selection, breeding, and domestication of a new cash cover crop for cold climates.
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Oakley CG, Lundemo S, Ågren J, Schemske DW. Heterosis is common and inbreeding depression absent in natural populations of
Arabidopsis thaliana. J Evol Biol 2019; 32:592-603. [DOI: 10.1111/jeb.13441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Affiliation(s)
| | - Sverre Lundemo
- Plant Ecology and Evolution Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Jon Ågren
- Plant Ecology and Evolution Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Douglas W. Schemske
- Department of Plant Biology W. K. Kellogg Biological Station Michigan State University East Lansing Michigan
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17
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Duruflé H, Ranocha P, Mbadinga Mbadinga DL, Déjean S, Bonhomme M, San Clemente H, Viudes S, Eljebbawi A, Delorme-Hinoux V, Sáez-Vásquez J, Reichheld JP, Escaravage N, Burrus M, Dunand C. Phenotypic Trait Variation as a Response to Altitude-Related Constraints in Arabidopsis Populations. FRONTIERS IN PLANT SCIENCE 2019; 10:430. [PMID: 31024596 PMCID: PMC6465555 DOI: 10.3389/fpls.2019.00430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/21/2019] [Indexed: 05/12/2023]
Abstract
UNLABELLED Natural variations help in identifying genetic mechanisms of morphologically and developmentally complex traits. Mountainous habitats provide an altitudinal gradient where one species encounters different abiotic conditions. We report the study of 341 individuals of Arabidopsis thaliana derived from 30 natural populations not belonging to the 1001 genomes, collected at increasing altitudes, between 200 and 1800 m in the Pyrenees. Class III peroxidases and ribosomal RNA sequences were used as markers to determine the putative genetic relationships among these populations along their altitudinal gradient. Using Bayesian-based statistics and phylogenetic analyses, these Pyrenean populations appear with significant divergence from the other regional accessions from 1001 genome (i.e., from north Spain or south France). Individuals of these populations exhibited varying phenotypic changes, when grown at sub-optimal temperature (22 vs. 15°C). These phenotypic variations under controlled conditions reflected intraspecific morphological variations. This study could bring new information regarding the west European population structure of A. thaliana and its phenotypic variations at different temperatures. The integrative analysis combining genetic, phenotypic variation and environmental datasets is used to analyze the acclimation of population in response to temperature changes. Regarding their geographical proximity and environmental diversity, these populations represent a tool of choice for studying plant response to temperature variation. HIGHLIGHTS -Studying the natural diversity of A. thaliana in the Pyrenees mountains helps to understand European population structure and to evaluate the phenotypic trait variation in response to climate change.
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Affiliation(s)
- Harold Duruflé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Philippe Ranocha
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Duchesse Lacour Mbadinga Mbadinga
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Sébastien Viudes
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Ali Eljebbawi
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
| | - Valerie Delorme-Hinoux
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France
| | - Nathalie Escaravage
- Université Toulouse 3 Paul Sabatier, CNRS, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Monique Burrus
- Université Toulouse 3 Paul Sabatier, CNRS, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Castanet Tolosan, France
- *Correspondence: Christophe Dunand,
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Fulgione A, Hancock AM. Archaic lineages broaden our view on the history of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 219:1194-1198. [PMID: 29862511 DOI: 10.1111/nph.15244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/25/2018] [Indexed: 05/15/2023]
Abstract
Contents Summary 1194 I. Introduction 1194 II. Origin of the A. thaliana species 1194 III. The classic model of the history of A. thaliana 1195 IV. New genomic data from outside Eurasia challenge our view of A. thaliana history 1195 V. Conclusions 1197 Acknowledgements 1197 References 1197 SUMMARY: Natural variation in Arabidopsis thaliana has contributed to discoveries in diverse areas of plant biology. While A. thaliana has typically been considered a weed associated primarily with human-mediated environments, including agricultural and urban sites and railways, it has recently been shown that it is also native in remote natural areas, including high altitude sites in Eurasia and Africa, from the Atlas mountains in Morocco to the afro-alpine regions in Eastern and South Africa to Yunnan in China, the Himalayas and the Tibetan Plateau. This finding suggests that while A. thaliana has been extensively studied in Europe and Western Asia there are still many open questions about its population history, genotype-phenotype relationships and mechanisms of adaptation.
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Affiliation(s)
- Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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Warmerdam S, Sterken MG, van Schaik C, Oortwijn MEP, Sukarta OCA, Lozano‐Torres JL, Dicke M, Helder J, Kammenga JE, Goverse A, Bakker J, Smant G. Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 218:724-737. [PMID: 29468687 PMCID: PMC6079644 DOI: 10.1111/nph.15034] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F-box family protein may function as (co-)regulators of susceptibility to M. incognita in Arabidopsis. Our data suggest that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.
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Affiliation(s)
- Sonja Warmerdam
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Mark G. Sterken
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Casper van Schaik
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Marian E. P. Oortwijn
- Laboratory of Plant BreedingWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Octavina C. A. Sukarta
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Jose L. Lozano‐Torres
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Johannes Helder
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Jan E. Kammenga
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Aska Goverse
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Jaap Bakker
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
| | - Geert Smant
- Laboratory of NematologyWageningen UniversityDroevendaalsesteeg 16708 PB Wageningenthe Netherlands
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Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol 2017; 18:239. [PMID: 29284515 PMCID: PMC5745794 DOI: 10.1186/s13059-017-1378-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
Background Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. Results We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. Conclusions A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.
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Cousins EA, Murren CJ. Edaphic history over seedling characters predicts integration and plasticity of integration across geologically variable populations of Arabidopsis thaliana. AMERICAN JOURNAL OF BOTANY 2017; 104:1802-1815. [PMID: 29196342 DOI: 10.3732/ajb.1700220] [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: 06/03/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Studies on phenotypic plasticity and plasticity of integration have uncovered functionally linked modules of aboveground traits and seedlings of Arabidopsis thaliana, but we lack details about belowground variation in adult plants. Functional modules can be comprised of additional suites of traits that respond to environmental variation. We assessed whether shoot and root responses to nutrient environments in adult A. thaliana were predictable from seedling traits or population-specific geologic soil characteristics at the site of origin. METHODS We compared 17 natural accessions from across the native range of A. thaliana using 14-day-old seedlings grown on agar or sand and plants grown to maturity across nutrient treatments in sand. We measured aboveground size, reproduction, timing traits, root length, and root diameter. Edaphic characteristics were obtained from a global-scale dataset and related to field data. KEY RESULTS We detected significant among-population variation in root traits of seedlings and adults and in plasticity in aboveground and belowground traits of adult plants. Phenotypic integration of roots and shoots varied by population and environment. Relative integration was greater in roots than in shoots, and integration was predicted by edaphic soil history, particularly organic carbon content, whereas seedling traits did not predict later ontogenetic stages. CONCLUSIONS Soil environment of origin has significant effects on phenotypic plasticity in response to nutrients, and on phenotypic integration of root modules and shoot modules. Root traits varied among populations in reproductively mature individuals, indicating potential for adaptive and integrated functional responses of root systems in annuals.
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Affiliation(s)
- Elsa A Cousins
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, USA
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts 01002, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, USA
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Masuda S, Nozawa K, Matsunaga W, Masuta Y, Kawabe A, Kato A, Ito H. Characterization of a heat-activated retrotransposon in natural accessions of Arabidopsis thaliana. Genes Genet Syst 2017; 91:293-299. [PMID: 27980240 DOI: 10.1266/ggs.16-00045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Natural accessions are used for studying intraspecies genetic variation in the model plant Arabidopsis thaliana in order to address fundamental questions of evolution. Transposable elements are responsible for a wide range of mutations and play significant roles in shaping a genome over evolutionary time. In the present study, we aimed to characterize ONSEN, a heat-activated long terminal repeat (LTR) retrotransposon, in natural A. thaliana accessions. Southern blot analysis demonstrated that ONSEN was present in all the studied accessions, but the copy number was diverse. Olympia-1 contained a single ONSEN copy, located in the centromere of Chromosome 3. A premature stop codon in Olympia-1 ONSEN presumably abolishes integrase activity, which in turn presumably renders the retrotransposon non-functional. Hybridization of Col-0 with Olympia-1 showed that several ONSEN copies in Col-0 were activated by heat stress and maintained their transpositional activity in the progeny.
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Affiliation(s)
| | | | | | | | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University
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African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:5213-5218. [PMID: 28473417 DOI: 10.1073/pnas.1616736114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120-90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.
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Andersen JC, Havill NP, Caccone A, Elkinton JS. Postglacial recolonization shaped the genetic diversity of the winter moth ( Operophtera brumata) in Europe. Ecol Evol 2017; 7:3312-3323. [PMID: 28515868 PMCID: PMC5433974 DOI: 10.1002/ece3.2860] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/20/2017] [Accepted: 01/28/2017] [Indexed: 12/05/2022] Open
Abstract
Changes in climate conditions, particularly during the Quaternary climatic oscillations, have long been recognized to be important for shaping patterns of species diversity. For species residing in the western Palearctic, two commonly observed genetic patterns resulting from these cycles are as follows: (1) that the numbers and distributions of genetic lineages correspond with the use of geographically distinct glacial refugia and (2) that southern populations are generally more diverse than northern populations (the “southern richness, northern purity” paradigm). To determine whether these patterns hold true for the widespread pest species the winter moth (Operophtera brumata), we genotyped 699 individual winter moths collected from 15 Eurasian countries with 24 polymorphic microsatellite loci. We find strong evidence for the presence of two major genetic clusters that diverged ~18 to ~22 ka, with evidence that secondary contact (i.e., hybridization) resumed ~ 5 ka along a well‐established hybrid zone in Central Europe. This pattern supports the hypothesis that contemporary populations descend from populations that resided in distinct glacial refugia. However, unlike many previous studies of postglacial recolonization, we found no evidence for the “southern richness, northern purity” paradigm. We also find evidence for ongoing gene flow between populations in adjacent Eurasian countries, suggesting that long‐distance dispersal plays an important part in shaping winter moth genetic diversity. In addition, we find that this gene flow is predominantly in a west‐to‐east direction, suggesting that recently debated reports of cyclical outbreaks of winter moth spreading from east to west across Europe are not the result of dispersal.
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Affiliation(s)
- Jeremy C Andersen
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA.,Present address: Jeremy C. Andersen, Department of Environmental Science Policy and Management University of California Berkeley Berkeley CA USA
| | | | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology Yale University New Haven CT USA
| | - Joseph S Elkinton
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
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25
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Lee CR, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova P, Alonso-Blanco C, Weigel D, Nordborg M. On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun 2017; 8:14458. [PMID: 28181519 PMCID: PMC5309843 DOI: 10.1038/ncomms14458] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/03/2017] [Indexed: 02/03/2023] Open
Abstract
Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these 'relicts' occupied post-glacial Eurasia first and were later replaced by the invading 'non-relicts', which expanded through the east-west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats.
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Affiliation(s)
- Cheng-Ruei Lee
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, 10617 Taipei, Taiwan
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Moises Exposito-Alonso
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Wei Ding
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Polina Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
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26
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Riewe D, Jeon HJ, Lisec J, Heuermann MC, Schmeichel J, Seyfarth M, Meyer RC, Willmitzer L, Altmann T. A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation, and is associated with metabolic and growth traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:826-838. [PMID: 27520391 DOI: 10.1111/tpj.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/13/2016] [Accepted: 08/05/2016] [Indexed: 05/05/2023]
Abstract
Fumarate and malate are known intermediates of the TCA cycle, a mitochondrial metabolic pathway generating NADH for respiration. Arabidopsis thaliana and other Brassicaceae contain an additional cytosolic fumarase (FUM2) that functions in carbon assimilation and nitrogen use. Here, we report the identification of a hitherto unknown FUM2 promoter insertion/deletion (InDel) polymorphism found between the Col-0 and C24 accessions, which also divides a large number of Arabidopsis accessions carrying either the Col-0 or the C24 allele. The polymorphism consists of two stretches of 2.1 and 3.8 kb, which are both absent from the promotor region of Col-0 FUM2. By analysing mutants as well as mapping and natural populations with contrasting FUM2 alleles, the promotor insertion was linked to reduced FUM2 mRNA expression, reduced fumarase activity and reduced fumarate/malate ratio in leaves. In a large population of 174 natural accessions, the polymorphism was also found to be associated with the fumarate/malate ratio, malate and fumarate levels, and with dry weight at 15 days after sowing (DAS). The association with biomass production was confirmed in an even larger (251) accession population for dry weight at 22 DAS. The dominant Col-0 allele that results in increased fumarate/malate ratios and enhanced biomass production is predominantly found in central/eastern European accessions, whereas the C24 type allele is prevalent on the Iberian Peninsula, west of the Rhine and in the British Isles. Our findings support the role of FUM2 in diurnal carbon storage, and point to a growth advantage of accessions carrying the FUM2 Col-0 allele.
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Affiliation(s)
- David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hea-Jung Jeon
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jan Lisec
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Judith Schmeichel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Monique Seyfarth
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Lothar Willmitzer
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
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Royer AM, Kremer C, George K, Pérez SG, Schemske DW, Conner JK. Incomplete loss of a conserved trait: function, latitudinal cline, and genetic constraints. Evolution 2016. [DOI: 10.1111/evo.13096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Anne M. Royer
- Department of Plant Biology and Kellogg Biological Station Michigan State University 3700 E. Gull Lake Dr. Hickory Corners Michigan 49060
| | - Colin Kremer
- Department of Ecology and Evolutionary Biology Yale University P. O. Box 208106 New Haven Connecticut 06520–8106
- Atmospheric and Oceanic Sciences Program Princeton University 300 Forrestal Road, Sayre Hall Princeton New Jersey 08544
| | - Kola George
- Department of Plant Biology and Kellogg Biological Station Michigan State University 3700 E. Gull Lake Dr. Hickory Corners Michigan 49060
- College of Charleston School of Sciences and Mathematics 66 George St. Charleston South Carolina 29424
| | - Samuel G. Pérez
- Department of Plant Biology and Kellogg Biological Station Michigan State University 3700 E. Gull Lake Dr. Hickory Corners Michigan 49060
| | - D. W. Schemske
- Department of Plant Biology and Kellogg Biological Station Michigan State University 3700 E. Gull Lake Dr. Hickory Corners Michigan 49060
| | - Jeffrey K. Conner
- Department of Plant Biology and Kellogg Biological Station Michigan State University 3700 E. Gull Lake Dr. Hickory Corners Michigan 49060
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28
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Gould BA, Stinchcombe JR. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana. Mol Ecol 2016; 26:92-106. [PMID: 27064998 DOI: 10.1111/mec.13643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
A long-standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole-genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common variants of large effect on flowering time in the native range do not appear to have been under recent strong selection in the introduced range. We identified a set of 38 new candidate genes that are putatively linked to the evolution of flowering time. A high degree of conditional neutrality of flowering time variants between the native and introduced range may preclude parallel evolution at the level of genes. Overall, neither gene pleiotropy nor available standing genetic variation appears to have restricted the evolution of flowering time to high-frequency variants from the native range or to known flowering time pathway genes.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
| | - John R Stinchcombe
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48823, USA
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29
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Sebasky ME, Keller SR, Taylor DR. Investigating past range dynamics for a weed of cultivation, Silene vulgaris. Ecol Evol 2016; 6:4800-11. [PMID: 27547314 PMCID: PMC4979708 DOI: 10.1002/ece3.2250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 11/05/2022] Open
Abstract
Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.
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Affiliation(s)
- Megan E Sebasky
- Department of Biology University of Virginia Charlottesville Virginia
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington Vermont
| | - Douglas R Taylor
- Department of Biology University of Virginia Charlottesville Virginia
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30
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Adams WW, Stewart JJ, Cohu CM, Muller O, Demmig-Adams B. Habitat Temperature and Precipitation of Arabidopsis thaliana Ecotypes Determine the Response of Foliar Vasculature, Photosynthesis, and Transpiration to Growth Temperature. FRONTIERS IN PLANT SCIENCE 2016; 7:1026. [PMID: 27504111 PMCID: PMC4959142 DOI: 10.3389/fpls.2016.01026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
Abstract
Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish) were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high) exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 and Swedish ecotypes, of phloem per minor vein in plants grown at the low temperature. In contrast, vein density and minor vein tracheary to sieve element ratio increased with increasing growth temperature - most strongly in Col-0 and least strongly in the Italian ecotype - and transpirational water loss correlated with vein density and number of tracheary elements per minor vein. Plotting of these vascular features as functions of climatic conditions in the habitat of origin suggested that temperatures during the evolutionary history of the ecotypes determined acclimatory responses of the foliar phloem and photosynthesis to temperature in this winter annual that upregulates photosynthesis in response to lower temperature, whereas the precipitation experienced during the evolutionary history of the ecotypes determined adjustment of foliar vein density, xylem, and transpiration to temperature. In particular, whereas photosynthetic capacity, leaf thickness, and foliar minor vein phloem features increased linearly with increasing latitude and decreasing temperature of the habitats of origin in response to experimental growth at low temperature, transpiration rate, foliar vein density, and minor vein tracheary element numbers and cross-sectional areas increased linearly with decreasing precipitation level in the habitats of origin in response to experimental growth at high temperature. This represents a situation where temperature acclimation of the apparent capacity for water flux through the xylem and transpiration rate in a winter annual responded differently from that of photosynthetic capacity, in contrast to previous reports of strong relationships between hydraulic conductance and photosynthesis in other studies.
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Affiliation(s)
- William W. Adams
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, USA
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31
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Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nägele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Picó FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salomé PA, Schmid KJ, Schmitz RJ, Seren Ü, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481-491. [PMID: 27293186 PMCID: PMC4949382 DOI: 10.1016/j.cell.2016.05.063] [Citation(s) in RCA: 723] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022]
Abstract
Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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32
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Monroe JG, McGovern C, Lasky JR, Grogan K, Beck J, McKay JK. Adaptation to warmer climates by parallel functional evolution of
CBF
genes in
Arabidopsis thaliana. Mol Ecol 2016; 25:3632-44. [DOI: 10.1111/mec.13711] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/20/2016] [Indexed: 01/05/2023]
Affiliation(s)
- J. Grey Monroe
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
| | - Cullen McGovern
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PA 16802 USA
| | - Kelsi Grogan
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - James Beck
- Department of Biological Sciences Wichita State University Wichita KS 67260 USA
- Botanical Research Institute of Texas Fort Worth TX 76107 USA
| | - John K. McKay
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
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Franzke A, Koch MA, Mummenhoff K. Turnip Time Travels: Age Estimates in Brassicaceae. TRENDS IN PLANT SCIENCE 2016; 21:554-561. [PMID: 26917156 DOI: 10.1016/j.tplants.2016.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/31/2016] [Indexed: 05/07/2023]
Abstract
Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Marcus A Koch
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany; Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, German
| | - Klaus Mummenhoff
- Biology Department, Botany, Osnabrück University, D-49069 Osnabrück, Germany
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Simon M, Durand S, Pluta N, Gobron N, Botran L, Ricou A, Camilleri C, Budar F. Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana. Genetics 2016; 203:1353-67. [PMID: 27182945 PMCID: PMC4937478 DOI: 10.1534/genetics.115.183707] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/28/2016] [Indexed: 11/18/2022] Open
Abstract
Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations.
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Affiliation(s)
- Matthieu Simon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Stéphanie Durand
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Natacha Pluta
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Nicolas Gobron
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Lucy Botran
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Anthony Ricou
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
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35
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc Natl Acad Sci U S A 2016; 113:3687-92. [PMID: 26979961 DOI: 10.1073/pnas.1520687113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the contribution of cytonuclear interactions to plant fitness variation is relatively well documented at the interspecific level, the prevalence of cytonuclear interactions at the intraspecific level remains poorly investigated. In this study, we set up a field experiment to explore the range of effects that cytonuclear interactions have on fitness-related traits in Arabidopsis thaliana To do so, we created a unique series of 56 cytolines resulting from cytoplasmic substitutions among eight natural accessions reflecting within-species genetic diversity. An assessment of these cytolines and their parental lines scored for 28 adaptive whole-organism phenotypes showed that a large proportion of phenotypic traits (23 of 28) were affected by cytonuclear interactions. The effects of these interactions varied from slight but frequent across cytolines to strong in some specific parental pairs. Two parental pairs accounted for half of the significant pairwise interactions. In one parental pair, Ct-1/Sha, we observed symmetrical phenotypic responses between the two nuclear backgrounds when combined with specific cytoplasms, suggesting nuclear differentiation at loci involved in cytonuclear epistasis. In contrast, asymmetrical phenotypic responses were observed in another parental pair, Cvi-0/Sha. In the Cvi-0 nuclear background, fecundity and phenology-related traits were strongly affected by the Sha cytoplasm, leading to a modified reproductive strategy without penalizing total seed production. These results indicate that natural variation in cytoplasmic and nuclear genomes interact to shape integrative traits that contribute to adaptation, thereby suggesting that cytonuclear interactions can play a major role in the evolutionary dynamics ofA. thaliana.
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Branham SE, Wright SJ, Reba A, Morrison GD, Linder CR. Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants. J Hered 2016; 107:257-65. [PMID: 26865732 DOI: 10.1093/jhered/esw008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/27/2016] [Indexed: 12/29/2022] Open
Abstract
Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions.
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Affiliation(s)
- Sandra E Branham
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX (Branham, Reba, and Linder); and Division of Plant Sciences, University of Missouri, Columbia, MO (Morrison).
| | - Sara J Wright
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX (Branham, Reba, and Linder); and Division of Plant Sciences, University of Missouri, Columbia, MO (Morrison)
| | - Aaron Reba
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX (Branham, Reba, and Linder); and Division of Plant Sciences, University of Missouri, Columbia, MO (Morrison)
| | - Ginnie D Morrison
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX (Branham, Reba, and Linder); and Division of Plant Sciences, University of Missouri, Columbia, MO (Morrison)
| | - C Randal Linder
- From the US Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414 (Branham); Department of Biology, Washington University, St. Louis, MO (Wright); Integrative Biology Department, University of Texas at Austin, Austin, TX (Branham, Reba, and Linder); and Division of Plant Sciences, University of Missouri, Columbia, MO (Morrison)
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Sexton JP, Hufford MB, C.Bateman A, Lowry DB, Meimberg H, Strauss SY, Rice KJ. Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses. Mol Ecol 2016; 25:911-28. [DOI: 10.1111/mec.13528] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/30/2015] [Accepted: 12/21/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Jason P. Sexton
- School of Natural Sciences University of California 5200 North Lake Rd. Merced CA 95343 USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution and Organismal Biology Iowa State University 339A Bessey Hall Ames IA 50011 USA
| | - Ashley C.Bateman
- Department of Biology Institute of Ecology and Evolution University of Oregon 77 Klamath Hall 1210 Eugene OR 97403 USA
| | - David B. Lowry
- Department of Plant Biology Michigan State University 612 Wilson Road East Lansing MI 48824 USA
| | - Harald Meimberg
- Institute of Integrative Nature Conservation Research University of Natural Resources and Life Sciences (Boku) Gregor Mendel‐Str. 33 1180 Vienna Austria
| | - Sharon Y. Strauss
- Department of Evolution and Ecology University of California One Shields Ave. Davis CA 95616 USA
| | - Kevin J. Rice
- Department of Plant Sciences University of California One Shields Ave. Davis CA 95616 USA
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Tyagi A, Singh S, Mishra P, Singh A, Tripathi AM, Jena SN, Roy S. Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient. AOB PLANTS 2015; 8:plv145. [PMID: 26672075 PMCID: PMC4719038 DOI: 10.1093/aobpla/plv145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/06/2015] [Indexed: 05/27/2023]
Abstract
The natural genetic variation within a plant species is primarily a consequence of its phylogeography and evolutionary history. This variation largely determines its present-day population structure. Arabidopsis thaliana, as a model plant, has been studied in great detail including its probable origin, local as well as global genetic diversity pattern, population structure, adaptation, etc. However, no such studies have so far been reported from the Indian Himalayan region. Here, we describe a comprehensive study on the genetic diversity and population structure of A. thaliana from an altitudinal range of 700-3400 m above mean sea level the highest altitudinal range reported so far. We also compare these populations with previously reported worldwide populations. A total of 48 accessions representing six populations were analysed using 19 microsatellites and 11 chloroplast markers. Genetic diversity analysis indicated populations to be highly diverse and comparable with worldwide populations. STRUCTURE, principal coordinate and isolation by distance (IBD) analyses showed that genetic variation in different populations is structured at geographical and altitudinal level. Further analyses indicate that these populations are genetically distinct from the rest of the world populations. Different parameters of the demographic expansion model support a rapid expansion. Based on mismatch distribution, the initial time of expansion of west Himalayan populations was found to be about 130 000 years. Bayesian analysis of divergence time indicated that these populations have a long evolutionary history in this region. Based on the results of genetic diversity parameters, demographic expansion and divergence time estimation, it appears that west Himalayan populations may be the source of the west-east expansion model.
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Affiliation(s)
- Antariksh Tyagi
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Shivani Singh
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India
| | - Parneeta Mishra
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India
| | - Akanksha Singh
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India
| | - Abhinandan Mani Tripathi
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India
| | - Satya Narayan Jena
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India
| | - Sribash Roy
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India Present address: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
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40
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Root architecture, plant size and soil nutrient variation in natural populations of Arabidopsis thaliana. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9808-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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41
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Botto JF. Plasticity to simulated shade is associated with altitude in structured populations of Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2015; 38:1321-32. [PMID: 25388923 DOI: 10.1111/pce.12481] [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: 08/22/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 05/26/2023]
Abstract
Plants compete for photosynthesis light and induce a shade avoidance syndrome (SAS) that confers an important advantage in asymmetric competition for light at high canopy densities. Shade plasticity was studied in a greenhouse experiment cultivating Arabidopsis thaliana plants from 15 populations spread across an altitudinal gradient in the northeast area of Spain that contain a high genetic variation into a reduced geographical range. Plants were exposed to sunlight or simulated shade to identify the range of shade plasticity. Fourteen vegetative, flowering and reproductive traits were measured throughout the life cycle. Shade plasticity in flowering time and dry mass was significantly associated with the altitude of population origin. Plants from coastal populations showed higher shade plasticity indexes than those from mountains. The altitudinal variation in flowering leaf plasticity adjusted negatively with average and minimum temperatures, whereas dry mass plasticity was better explained by negative regressions with the average, maximum and minimum temperatures, and by a positive regression with average precipitation of the population origin. The lack of an altitudinal gradient for the widest number of traits suggests that shade light could be a driver explaining the distribution pattern of individuals in smaller geographical scales than those explored here.
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Affiliation(s)
- Javier F Botto
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas, Av. San Martín 4453, C1417DSE, Ciudad de Buenos Aires, Argentina
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42
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Krämer U. Planting molecular functions in an ecological context with Arabidopsis thaliana. eLife 2015; 4:e06100. [PMID: 25807084 PMCID: PMC4373673 DOI: 10.7554/elife.06100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/13/2015] [Indexed: 12/31/2022] Open
Abstract
The vascular plant Arabidopsis thaliana is a central genetic model and universal reference organism in plant and crop science. The successful integration of different fields of research in the study of A. thaliana has made a large contribution to our molecular understanding of key concepts in biology. The availability and active development of experimental tools and resources, in combination with the accessibility of a wealth of cumulatively acquired knowledge about this plant, support the most advanced systems biology approaches among all land plants. Research in molecular ecology and evolution has also brought the natural history of A. thaliana into the limelight. This article showcases our current knowledge of the natural history of A. thaliana from the perspective of the most closely related plant species, providing an evolutionary framework for interpreting novel findings and for developing new hypotheses based on our knowledge of this plant.
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Affiliation(s)
- Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Bochum, Germany
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43
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Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana. Heredity (Edinb) 2015; 115:73-82. [PMID: 26059971 DOI: 10.1038/hdy.2015.18] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 02/09/2015] [Accepted: 02/18/2015] [Indexed: 02/03/2023] Open
Abstract
Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.
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44
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Hamilton JA, Okada M, Korves T, Schmitt J. The role of climate adaptation in colonization success inArabidopsis thaliana. Mol Ecol 2015; 24:2253-63. [DOI: 10.1111/mec.13099] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Jill A. Hamilton
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Miki Okada
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
| | - Tonia Korves
- Data Analytics Department; The MITRE Corporation; 202 Burlington Rd, Bedford MA 01730 USA
| | - Johanna Schmitt
- Department of Evolution and Ecology; University of California; Davis CA 95616 USA
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45
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Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, Guo YL. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd's purse (Capsella bursa-pastoris). MOLECULAR PLANT 2015; 8:427-438. [PMID: 25661060 DOI: 10.1016/j.molp.2014.11.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/19/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Adaptation is the most important ability for organisms to survive in diverse habitats. Animals have the option to escape from stressful environments, but plants do not. In plants, polyploids consist of about 30%-70% angiosperms and 95% ferns, of which some are important crops such as cotton and wheat. How polyploid plants adapt to various habitats has been a fundamental question remained largely unanswered. The tetraploid Shepherd's purse (Capsella bursa-pastoris) is one of the most successful plants on earth and has been distributed across the world, thus being an ideal model system for studying the adaptation of polyploids. We found that there are frequent introgressions from congeneric diploids to Shepherd's purse. Ecological niche modeling suggests that ecological differentiation is evident between the introgressed and non-introgressed C. bursa-pastoris, and the introgressions are a source of adaptation. This result links an evolutionary process to the adaptation of polyploids, and sheds light on the breeding strategy of polyploids as well. We conclude that frequent introgressions from congeneric diploids contributed to the acquisition of adequate genetic variations, thereby allowing C. bursa-pastoris to adapt to various habitats across the world. Our results highlight how a polyploid could have successfully established after it originated.
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Affiliation(s)
- Ting-Shen Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Wen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu-Pan Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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46
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Oakley CG, Ågren J, Atchison RA, Schemske DW. QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs. Mol Ecol 2014; 23:4304-15. [DOI: 10.1111/mec.12862] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/11/2014] [Accepted: 07/16/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Christopher G. Oakley
- Department of Plant Biology; Michigan State University; East Lansing MI 48824-1312 USA
| | - Jon Ågren
- Department of Plant Ecology and Evolution; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18 D SE-752 36 Uppsala Sweden
| | - Rachel A. Atchison
- Department of Plant Biology; Michigan State University; East Lansing MI 48824-1312 USA
| | - Douglas W. Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station; Michigan State University; East Lansing MI 48824 USA
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47
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Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: searching for G×E effects. G3-GENES GENOMES GENETICS 2014; 4:1465-78. [PMID: 24902604 PMCID: PMC4132177 DOI: 10.1534/g3.114.012427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the natural world, genotype expression is influenced by an organism’s environment. Identifying and understanding the genes underlying phenotypes in different environments is important for making advances in fields ranging from evolution to medicine to agriculture. With the availability of genome-wide genetic-marker datasets, it is possible to look for genes that interact with the environment. Using the model organism, Arabidopsis thaliana, we looked for genes underlying phenotypes as well as genotype-by-environment interactions in four germination traits under two light and two nutrient conditions. We then performed genome-wide association tests to identify candidate genes underlying the observed phenotypes and genotype-by-environment interactions. Of the four germination traits examined, only two showed significant genotype-by-environment interactions. While genome-wide association analyses did not identify any markers or genes explicitly linked to genotype-by-environment interactions, we did identify a total of 55 markers and 71 genes associated with germination differences. Of the 71 genes, four—ZIGA4, PS1, TOR, and TT12—appear to be strong candidates for further study of germination variation under different environments.
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48
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Wilczek AM, Cooper MD, Korves TM, Schmitt J. Lagging adaptation to warming climate in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2014; 111:7906-13. [PMID: 24843140 PMCID: PMC4050579 DOI: 10.1073/pnas.1406314111] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species' native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species' native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.
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Affiliation(s)
- Amity M Wilczek
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Department of Natural Sciences, Deep Springs College, Big Pine, CA 93513
| | - Martha D Cooper
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912
| | - Tonia M Korves
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Data Analytics Department, The MITRE Corporation, Bedford, MA 01730-1420; and
| | - Johanna Schmitt
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;Department of Evolution and Ecology, University of California, Davis, CA 95616
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49
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Falahati-Anbaran M, Lundemo S, Stenøien HK. Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 202:1043-1054. [PMID: 24471774 DOI: 10.1111/nph.12702] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/19/2013] [Indexed: 06/03/2023]
Abstract
Plants may escape unfavorable environments by dispersing to new sites, or by remaining in an ungerminated state at a given site until environmental conditions become favorable. There is limited evidence regarding the occurrence, interplay and relative importance of dispersal processes in time and space in plant populations. Thirty-six natural populations of the annual ruderal species Arabidopsis thaliana were monitored over five consecutive years, sampling both seed bank and above-ground cohorts. We show that immigration rates are considerably higher than previously inferred, averaging 1.7% per population yr(-1). On the other hand, almost one-third of the individuals in a given above-ground cohort result from seeds shed 2 or 3 yr back in time in 10 of the studied populations. Populations that disappeared one year were recolonized by regeneration from the seed bank the subsequent year. Thus, dispersal in both time and space is an important contributor to the structuring of genetic variability in natural populations of A. thaliana, where a high dispersal rate in time may partly counteract the homogenizing effects of spatial seed and pollen dispersal.
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Affiliation(s)
- Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
- NTNU University Museum, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
- School of Biology, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Sverre Lundemo
- Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
- NTNU University Museum, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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Vekemans X, Poux C, Goubet PM, Castric V. The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? J Evol Biol 2014; 27:1372-85. [PMID: 24725152 DOI: 10.1111/jeb.12372] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the 'mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants.
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Affiliation(s)
- X Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université Lille 1, Villeneuve d'Ascq Cedex, France
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