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Genetic architecture of a plant adaptive trait: QTL mapping of intraspecific variation for tolerance to metal pollution in Arabidopsis halleri. Heredity (Edinb) 2019; 122:877-892. [PMID: 30670845 DOI: 10.1038/s41437-019-0184-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/01/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Anthropogenic activities are among the main drivers of global change and result in drastic habitat modifications, which represent strong evolutionary challenges for biological species that can either migrate, adapt, or disappear. In this context, understanding the genetics of adaptive traits is a prerequisite to enable long-term maintenance of populations under strong environmental constraints. To examine these processes, a QTL approach was developed here using the pseudometallophyte Arabidopsis halleri, which displays among-population adaptive divergence for tolerance to metallic pollution in soils. An F2 progeny was obtained by crossing individuals from metallicolous and non-metallicolous populations from Italian Alps, where intense metallurgic activities have created strong landscape heterogeneity. Then, we combined genome de novo assembly and genome resequencing of parental genotypes to obtain single-nucleotide polymorphism markers and achieve high-throughput genotyping of the progeny. QTL analysis was performed using growth parameters and photosynthetic yield to assess zinc tolerance levels. One major QTL was identified for photosynthetic yield. It explained about 27% of the phenotypic variance. Functional annotation of the QTL and gene expression analyses highlighted putative candidate genes. Our study represents a successful approach combining evolutionary genetics and advanced molecular tools, helping to better understand how a species can face new selective pressures of anthropogenic origin.
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Merlot S, Sanchez Garcia de la Torre V, Hanikenne M. Physiology and Molecular Biology of Trace Element Hyperaccumulation. AGROMINING: FARMING FOR METALS 2018. [DOI: 10.1007/978-3-319-61899-9_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Hörger AC, Fones HN, Preston GM. The current status of the elemental defense hypothesis in relation to pathogens. FRONTIERS IN PLANT SCIENCE 2013; 4:395. [PMID: 24137169 PMCID: PMC3797420 DOI: 10.3389/fpls.2013.00395] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/16/2013] [Indexed: 05/08/2023]
Abstract
Metal hyperaccumulating plants are able to accumulate exceptionally high concentrations of metals, such as zinc, nickel, or cadmium, in their aerial tissues. These metals reach concentrations that would be toxic to most other plant species. This trait has evolved multiple times independently in the plant kingdom. Recent studies have provided new insight into the ecological and evolutionary significance of this trait, by showing that some metal hyperaccumulating plants can use high concentrations of accumulated metals to defend themselves against attack by pathogenic microorganisms and herbivores. Here, we review the evidence that metal hyperaccumulation acts as a defensive trait in plants, with particular emphasis on plant-pathogen interactions. We discuss the mechanisms by which defense against pathogens might have driven the evolution of metal hyperaccumulation, including the interaction of this trait with other forms of defense. In particular, we consider how physiological adaptations and fitness costs associated with metal hyperaccumulation could have resulted in trade-offs between metal hyperaccumulation and other defenses. Drawing on current understanding of the population ecology of metal hyperaccumulator plants, we consider the conditions that might have been necessary for metal hyperaccumulation to be selected as a defensive trait, and discuss the likelihood that these were fulfilled. Based on these conditions, we propose a possible scenario for the evolution of metal hyperaccumulation, in which selective pressure for resistance to pathogens or herbivores, combined with gene flow from non-metallicolous populations, increases the likelihood that the metal hyperaccumulating trait becomes established in plant populations.
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Affiliation(s)
- Anja C. Hörger
- Department of Plant Sciences, University of OxfordOxford, UK
| | - Helen N. Fones
- Department of Plant Sciences, University of OxfordOxford, UK
| | - Gail M. Preston
- Department of Plant Sciences, University of OxfordOxford, UK
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Pauwels M, Vekemans X, Godé C, Frérot H, Castric V, Saumitou-Laprade P. Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance, Arabidopsis halleri (Brassicaceae). THE NEW PHYTOLOGIST 2012; 193:916-928. [PMID: 22225532 DOI: 10.1111/j.1469-8137.2011.04003.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arabidopsis halleri is a pseudometallophyte involved in numerous molecular studies of the adaptation to anthropogenic metal stress. In order to test the representativeness of genetic accessions commonly used in these studies, we investigated the A. halleri population genetic structure in Europe. Microsatellite and nucleotide polymorphisms from the nuclear and chloroplast genomes, respectively, were used to genotype 65 populations scattered over Europe. The large-scale population structure was characterized by a significant phylogeographic signal between two major genetic units. The localization of the phylogeographic break was assumed to result from vicariance between large populations isolated in southern and central Europe, on either side of ice sheets covering the Alps during the Quaternary ice ages. Genetic isolation was shown to be maintained in western Europe by the high summits of the Alps, whereas admixture was detected in the Carpathians. Considering the phylogeographic literature, our results suggest a distinct phylogeographic pattern for European species occurring in both mountain and lowland habitats. Considering the evolution of metal adaptation in A. halleri, it appears that recent adaptations to anthropogenic metal stress that have occurred within either phylogeographic unit should be regarded as independent events that potentially have involved the evolution of a variety of genetic mechanisms.
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Affiliation(s)
- Maxime Pauwels
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Xavier Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Cécile Godé
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Hélène Frérot
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Vincent Castric
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Pierre Saumitou-Laprade
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
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Hanikenne M, Nouet C. Metal hyperaccumulation and hypertolerance: a model for plant evolutionary genomics. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:252-9. [PMID: 21531166 DOI: 10.1016/j.pbi.2011.04.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/04/2011] [Accepted: 04/07/2011] [Indexed: 05/21/2023]
Abstract
In the course of evolution, plants adapted to widely differing metal availabilities in soils and therefore represent an important source of natural variation of metal homeostasis networks. Research on plant metal homeostasis can thus provide insights into the functioning, regulation and adaptation of biological networks. Here, we describe major recent breakthroughs in the understanding of the genetic and molecular basis of metal hyperaccumulation and associated hypertolerance, a naturally selected complex trait which represents an extreme adaptation of the metal homeostasis network. Investigations in this field reveal further the molecular alterations underlying the evolution of natural phenotypic diversity and provide a highly relevant framework for comparative genomics.
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Affiliation(s)
- Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering, Department of Life Sciences (B22), University of Liège, Liège, Belgium.
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Budar F, Roux F. The role of organelle genomes in plant adaptation: time to get to work! PLANT SIGNALING & BEHAVIOR 2011; 6:635-9. [PMID: 21499027 PMCID: PMC3172827 DOI: 10.4161/psb.6.5.14524] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 01/28/2011] [Indexed: 05/25/2023]
Abstract
That organellar genome variation can play a role in plant adaptation has been suggested by several lines of evidence, including cytoplasm capture, cytoplasm effects in local adaptation, and positive selection in a chloroplast gene. In-depth analysis and better understanding of the genetic basis of plant adaptation is becoming a main objective in plant science. Arabidopsis thaliana has all the required characteristics to be used as a model for obtaining knowledge on the mechanisms underlying the role of organelles in plant adaptation. The availability of the appropriate tools and materials for assessing organelle genetic variation will open up new opportunities for developing novel breeding strategies.
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Affiliation(s)
- Françoise Budar
- INRA, Institut Jean-Pierre Bourgin, Versailles cedex, France.
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Burgess RM, Ho KT, Biales AD, Brack W. Recent Developments in Whole Sediment Toxicity Identification Evaluations: Innovations in Manipulations and Endpoints. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2011. [DOI: 10.1007/978-3-642-18384-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Maestri E, Marmiroli N. Transgenic plants for phytoremediation. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2011; 13 Suppl 1:264-279. [PMID: 22046764 DOI: 10.1080/15226514.2011.568549] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phytoremediation is a green, sustainable and promising solution to problems of environmental contamination. It entails the use of plants for uptake, sequestration, detoxification or volatilization of inorganic and organic pollutants from soils, water, sediments and possibly air. Phytoremediation was born from the observation that plants possessed physiological properties useful for environmental remediation. This was shortly followed by the application of breeding techniques and artificial selection to genetically improve some of the more promising and interesting species. Now, after nearly 20 years of research, transgenic plants for phytoremediation have been produced, but none have reached commercial existence. Three main approaches have been developed: (1) transformation with genes from other organisms (mammals, bacteria, etc.); (2) transformation with genes from other plant species; and (3) overexpression of genes from the same plant species. Many encouraging results have been reported, even though in some instances results have been contrary to expectations. This review will illustrate the main examples with a critical discussion of what we have learnt from them.
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Affiliation(s)
- Elena Maestri
- Department of Environmental Sciences, University of Parma, Parma, Italy.
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Frérot H, Faucon MP, Willems G, Godé C, Courseaux A, Darracq A, Verbruggen N, Saumitou-Laprade P. Genetic architecture of zinc hyperaccumulation in Arabidopsis halleri: the essential role of QTL x environment interactions. THE NEW PHYTOLOGIST 2010; 187:355-367. [PMID: 20487314 DOI: 10.1111/j.1469-8137.2010.03295.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This study sought to determine the main genomic regions that control zinc (Zn) hyperaccumulation in Arabidopsis halleri and to examine genotype x environment effects on phenotypic variance. To do so, quantitative trait loci (QTLs) were mapped using an interspecific A. halleri x Arabidopsis lyrata petraea F(2) population. *The F(2) progeny as well as representatives of the parental populations were cultivated on soils at two different Zn concentrations. A linkage map was constructed using 70 markers. *In both low and high pollution treatments, zinc hyperaccumulation showed high broad-sense heritability (81.9 and 74.7%, respectively). Five significant QTLs were detected: two QTLs specific to the low pollution treatment (chromosomes 1 and 4), and three QTLs identified at both treatments (chromosomes 3, 6 and 7). These QTLs explained 50.1 and 36.5% of the phenotypic variance in low and high pollution treatments, respectively. Two QTLs identified at both treatments (chromosomes 3 and 6) showed significant QTL x environment interactions. *The QTL on chromosome 3 largely colocalized with a major QTL previously identified for Zn and cadmium (Cd) tolerance. This suggests that Zn tolerance and hyperaccumulation share, at least partially, a common genetic basis and may have simultaneously evolved on heavy metal-contaminated soils.
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Affiliation(s)
- Hélène Frérot
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Michel-Pierre Faucon
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Glenda Willems
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Cécile Godé
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Adeline Courseaux
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Aude Darracq
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
| | - Nathalie Verbruggen
- Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles, Campus de la Plaine, CP242, boulevard du Triomphe, 1050 Bruxelles, Belgium
| | - Pierre Saumitou-Laprade
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, F-59655 Villeneuve d'Ascq Cedex, France
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Ritter A, Ubertini M, Romac S, Gaillard F, Delage L, Mann A, Cock JM, Tonon T, Correa JA, Potin P. Copper stress proteomics highlights local adaptation of two strains of the model brown alga Ectocarpus siliculosus. Proteomics 2010; 10:2074-88. [PMID: 20373519 DOI: 10.1002/pmic.200900004] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 11/19/2009] [Indexed: 11/10/2022]
Abstract
Ectocarpus siliculosus is a cosmopolitan brown alga with capacity to thrive in copper enriched environments. Analysis of copper toxicity was conducted in two strains of E. siliculosus isolated from (i) an uncontaminated coast in southern Peru (Es32) and (ii) a copper polluted rocky beach in northern Chile (Es524). Es32 was more sensitive than Es524, with toxicity detected at 50 microg/L Cu, whereas Es524 displayed negative effects only when exposed to 250 microg/L Cu. Differential soluble proteome profiling for each strain exposed to sub-lethal copper levels allowed to identify the induction of proteins related to processes such as energy production, glutathione metabolism as well as accumulation of HSPs. In addition, the inter-strain comparison of stress-related proteomes led to identify features related to copper tolerance in Es524, such as striking expression of a PSII Mn-stabilizing protein and a Fucoxanthine chlorophyll a-c binding protein. Es524 also expressed specific stress-related enzymes such as RNA helicases from the DEAD box families and a vanadium-dependent bromoperoxidase. These observations were supported by RT-qPCR for some of the identified genes and an enzyme activity assay for vanadium-dependent bromoperoxidase. Therefore, the occurrence of two different phenotypes within two distinct E. siliculosus strains studied at the physiological and proteomic levels strongly suggest that persistent copper stress may represent a selective force leading to the development of strains genetically adapted to copper contaminated sites.
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Affiliation(s)
- Andrés Ritter
- Université Pierre et Marie Curie-Paris 6, Végétaux Marins et Biomolécules, Station Biologique, Place Georges Teissier, Roscoff, France
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Lowry DB, Hall MC, Salt DE, Willis JH. Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inland Mimulus guttatus. THE NEW PHYTOLOGIST 2009; 183:776-788. [PMID: 19549130 DOI: 10.1111/j.1469-8137.2009.02901.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Local adaptation is a well-established phenomenon whereby habitat-mediated natural selection drives the differentiation of populations. However, little is known about how specific traits and loci combine to cause local adaptation. Here, we conducted a set of experiments to determine which physiological mechanisms contribute to locally adaptive divergence in salt tolerance between coastal perennial and inland annual ecotypes of Mimulus guttatus. Quantitative trait locus (QTL) mapping was used to discover loci involved in salt spray tolerance and leaf sodium (Na(+)) concentration. To determine whether these QTLs confer fitness in the field, we examined their effects in reciprocal transplant experiments using recombinant inbred lines (RILs). Coastal plants had constitutively higher leaf Na(+) concentrations and greater levels of tissue tolerance, but no difference in osmotic stress tolerance. Three QTLs contributed to salt spray tolerance and two QTLs to leaf Na(+) concentration. All three salt-spray tolerance QTLs had a significant fitness effects at the coastal field site but no effects inland. Leaf Na(+) QTLs had no detectable fitness effects in the field. * Physiological results are consistent with adaptation of coastal populations to salt spray and soil salinity. Field results suggest that there may not be trade-offs across habitats for alleles involved in local salt spray adaptations.
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Affiliation(s)
- David B Lowry
- University Program in Genetics and Genomics, Box 3565 Duke University Medical Center, Durham, NC 27710, USA
- Department of Biology, Box 90338, Duke University, Durham NC 27708, USA
| | - Megan C Hall
- Center for Genomics and Systems Biology, Department of Biology, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - David E Salt
- Horticultural and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - John H Willis
- University Program in Genetics and Genomics, Box 3565 Duke University Medical Center, Durham, NC 27710, USA
- Department of Biology, Box 90338, Duke University, Durham NC 27708, USA
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de Meaux J, Koornneef M. The cause and consequences of natural variation: the genome era takes off! CURRENT OPINION IN PLANT BIOLOGY 2008; 11:99-102. [PMID: 18337159 DOI: 10.1016/j.pbi.2008.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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