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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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Mahmoudi N, Cruz C, Mahdhi M, Mars M, Caeiro MF. Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions. PeerJ 2019; 7:e6401. [PMID: 30842895 PMCID: PMC6398376 DOI: 10.7717/peerj.6401] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/05/2019] [Indexed: 11/20/2022] Open
Abstract
Mycorrhizal symbioses are considered indicators of ecosystem biodiversity. However, their diversity and relevance in arid and semi-arid ecosystems are poorly understood. This study addressed this subject, the main objective being to evaluate arbuscular mycorrhizal fungi (AMF) diversity and heterogeneity in a semi-arid region. Samples of bulk and rhizosphere soil and fine roots of Medicago truncatula were collected at four different sites with the same aridity index (6.1), in Bou-Hedma National Park, Tunisia, a semi-arid ecosystem. AMF taxa were assessed by 454- pyrosequencing and identified by BLAST matching of operational taxonomic units (OTUs) against the MaarjAM database, targeting AMF SSU rRNA gene diversity. Roots were the hotspots of AMF diversity (107 OTUs out of a total of 138). Of the 138 OTUs, 113 found correspondence in the MaarjAM database, with 32 AMF virtual taxa (VTX),19 Site-exclusive (SE) and 13 common to at least two sites (Non-site exclusive, NSE); the remaining 25 OTUs grouped in 16 putative new AMF taxa (pNTX), each one consisting of OTUs sharing pairwise distances not higher than 3%. We found a high diversity and heterogeneity of AMF across the four sites, which showed, in a regression analysis, significant relation to six out of the eight environmental parameters evaluated: grazing activity and soil texture, electrical conductivity, organic matter, total phosphorus and total nitrogen. AMF colonization of plants also presented significant differences among the four sites, as well as spore density, microbial biomass and several enzymatic activities (dehydrogenase, β-glucosidase and phosphatase) evaluated in rhizosphere soils. The four sites clustered in two groups in a hierarchical clustering evaluation based on their AMF diversity (total numbers of OTU, VTX and pNTX) and the parameters referred above. The crucial role of abiotic factors, other than aridity index, on AMF community composition, was evidenced by the high heterogeneity found between AMF communities across sites under identical aridity conditions.
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Affiliation(s)
- Neji Mahmoudi
- Faculté des Sciences de Gabès, Unité de recherche, Biodiversité et Valorisation des Bio-ressources en Zones Arides (BVBZA), Erriadh Zrig, Tunisie
| | - Cristina Cruz
- Faculdade de Ciências da Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes (cE3c), Lisboa, Portugal
| | - Mosbah Mahdhi
- Center for Environmental Research and Studies, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Mohamed Mars
- Faculté des Sciences de Gabès, Unité de recherche, Biodiversité et Valorisation des Bio-ressources en Zones Arides (BVBZA), Erriadh Zrig, Tunisie
| | - Maria F. Caeiro
- Faculdade de Ciências da Universidade de Lisboa, Centro de Estudos do Ambiente e do Mar (CESAM), Lisboa, Portugal
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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Ben Abdallah H, Mai HJ, Slatni T, Fink-Straube C, Abdelly C, Bauer P. Natural Variation in Physiological Responses of Tunisian Hedysarum carnosum Under Iron Deficiency. FRONTIERS IN PLANT SCIENCE 2018; 9:1383. [PMID: 30333841 PMCID: PMC6176081 DOI: 10.3389/fpls.2018.01383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 08/30/2018] [Indexed: 05/31/2023]
Abstract
Iron (Fe) is an essential element for plant growth and development. The cultivation of leguminous plants has generated strong interest because of their growth even on poor soils. Calcareous and saline soils with poor mineral availability are wide-spread in Tunisia. In an attempt to select better forage crops adapted to Tunisian soils, we characterized Fe deficiency responses of three different isolates of Hedysarum carnosum, an endemic Tunisian extremophile species growing in native stands in salt and calcareous soil conditions. H. carnosum is a non-model crop. The three isolates, named according to their habitats Karkar, Thelja, and Douiret, differed in the expression of Fe deficiency symptoms like morphology, leaf chlorosis with compromised leaf chlorophyll content and photosynthetic capacity and leaf metal contents. Across these parameters Thelja was found to be tolerant, while Karkar and Douiret were susceptible to Fe deficiency stress. The three physiological and molecular indicators of the iron deficiency response in roots, Fe reductase activity, growth medium acidification and induction of the IRON-REGULATED TRANSPORTER1 homolog, indicated that all lines responded to -Fe, however, varied in the strength of the different responses. We conclude that the individual lines have distinct adaptation capacities to react to iron deficiency, presumably involving mechanisms of whole-plant iron homeostasis and internal metal distribution. The Fe deficiency tolerance of Thelja might be linked with adaptation to its natural habitat on calcareous soil.
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Affiliation(s)
| | - Hans Jörg Mai
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tarek Slatni
- Laboratory of Extremophile Plant, Center of Biotechnology of Borj Cedria, Hammam-Lif, Tunisia
| | | | - Chedly Abdelly
- Laboratory of Extremophile Plant, Center of Biotechnology of Borj Cedria, Hammam-Lif, Tunisia
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
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Functional Genomics and Flowering Time in Medicago truncatula: An Overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1822:261-271. [PMID: 30043309 DOI: 10.1007/978-1-4939-8633-0_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Flowering time is an important trait that influences adaptation and yield in many crop legumes. Both the inherent earliness of flowering and the degree to which it is responsive to environmental factors determine both the eco-geographic range across which crops can be successfully grown and the seasonal cycles most suitable for production. This chapter will provide a brief review of studies investigating the genetic control of flowering time in Medicago truncatula.
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Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:887-901. [PMID: 29353413 PMCID: PMC5852200 DOI: 10.1007/s00122-017-3045-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East-West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables. Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Bhavna Hurgobin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | | | - Lars G. Kamphuis
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Jens D. Berger
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - James K. Hane
- CCDM Bioinformatics, Centre for Crop Disease Management, Curtin University, Bentley, WA 6102 Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Matthew N. Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
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Berthouly-Salazar C, Thuillet AC, Rhoné B, Mariac C, Ousseini IS, Couderc M, Tenaillon MI, Vigouroux Y. Genome scan reveals selection acting on genes linked to stress response in wild pearl millet. Mol Ecol 2016; 25:5500-5512. [PMID: 27664976 DOI: 10.1111/mec.13859] [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: 04/27/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
Abstract
Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two-step strategy to limit false-positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods-three based on differentiation among populations and one based on diversity patterns within populations-to identify outlier SNPs from a set of 87 218 high-quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses.
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Affiliation(s)
- Cécile Berthouly-Salazar
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France. .,LMI LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal.
| | - Anne-Céline Thuillet
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France
| | - Bénédicte Rhoné
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France.,Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Cédric Mariac
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France
| | - Issaka Salia Ousseini
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France
| | - Marie Couderc
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France
| | - Maud I Tenaillon
- Génétique Quantitative et Evolution - Le Moulon, INRA - Université Paris-Sud - CNRS - AgroParisTech, Université Paris-Saclay, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), 34394, Montpellier Cedex 5, France
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Moriuchi KS, Friesen ML, Cordeiro MA, Badri M, Vu WT, Main BJ, Aouani ME, Nuzhdin SV, Strauss SY, von Wettberg EJB. Salinity Adaptation and the Contribution of Parental Environmental Effects in Medicago truncatula. PLoS One 2016; 11:e0150350. [PMID: 26943813 PMCID: PMC4778912 DOI: 10.1371/journal.pone.0150350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 02/14/2016] [Indexed: 11/19/2022] Open
Abstract
High soil salinity negatively influences plant growth and yield. Some taxa have evolved mechanisms for avoiding or tolerating elevated soil salinity, which can be modulated by the environment experienced by parents or offspring. We tested the contribution of the parental and offspring environments on salinity adaptation and their potential underlying mechanisms. In a two-generation greenhouse experiment, we factorially manipulated salinity concentrations for genotypes of Medicago truncatula that were originally collected from natural populations that differed in soil salinity. To compare population level adaptation to soil salinity and to test the potential mechanisms involved we measured two aspects of plant performance, reproduction and vegetative biomass, and phenological and physiological traits associated with salinity avoidance and tolerance. Saline-origin populations had greater biomass and reproduction under saline conditions than non-saline populations, consistent with local adaptation to saline soils. Additionally, parental environmental exposure to salt increased this difference in performance. In terms of environmental effects on mechanisms of salinity adaptation, parental exposure to salt spurred phenological differences that facilitated salt avoidance, while offspring exposure to salt resulted in traits associated with greater salt tolerance. Non-saline origin populations expressed traits associated with greater growth in the absence of salt while, for saline adapted populations, the ability to maintain greater performance in saline environments was also associated with lower growth potential in the absence of salt. Plastic responses induced by parental and offspring environments in phenology, leaf traits, and gas exchange contribute to salinity adaptation in M. truncatula. The ability of plants to tolerate environmental stress, such as high soil salinity, is likely modulated by a combination of parental effects and within-generation phenotypic plasticity, which are likely to vary in populations from contrasting environments.
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Affiliation(s)
- Ken S. Moriuchi
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Maren L. Friesen
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
- Department of Plant Biology, Michigan State University, Lansing, Michigan 48824, United States of America
| | - Matilde A. Cordeiro
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Plant Cell Biotechnology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mounawer Badri
- Centre of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif, Tunisia
| | - Wendy T. Vu
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Bradley J. Main
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | | | - Sergey V. Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Sharon Y. Strauss
- Department of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, United States of America
| | - Eric J. B. von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, Florida, United States of America
- Kushlan Institute for Tropical Science, Fairchild Tropical Botanic Garden, Coral Gables, Florida, United States of America
- * E-mail:
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Abstract
Darwin's theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.
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Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria;
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10
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Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:269. [PMID: 25954294 PMCID: PMC4404971 DOI: 10.3389/fpls.2015.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/03/2015] [Indexed: 05/05/2023]
Abstract
Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Cécile Ben
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Martina Rickauer
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Nevin D. Young
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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11
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Vu WT, Chang PL, Moriuchi KS, Friesen ML. Genetic variation of transgenerational plasticity of offspring germination in response to salinity stress and the seed transcriptome of Medicago truncatula. BMC Evol Biol 2015; 15:59. [PMID: 25884157 PMCID: PMC4406021 DOI: 10.1186/s12862-015-0322-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transgenerational plasticity provides phenotypic variation that contributes to adaptation. For plants, the timing of seed germination is critical for offspring survival in stressful environments, as germination timing can alter the environmental conditions a seedling experiences. Stored seed transcripts are important determinants of seed germination, but have not previously been linked with transgenerational plasticity of germination behavior. In this study we used RNAseq and growth chamber experiments of the model legume M. trucantula to test whether parental exposure to salinity stress influences the expression of stored seed transcripts and early offspring traits and test for genetic variation. RESULTS We detected genotype-dependent parental environmental effects (transgenerational plasticity) on the expression levels of stored seed transcripts, seed size, and germination behavior of four M. truncatula genotypes. More than 50% of the transcripts detected in the mature, ungerminated seed transcriptome were annotated as regulating seed germination, some of which are involved in abiotic stress response and post-embryonic development. Some genotypes showed increased seed size in response to parental exposure to salinity stress, but no parental environmental influence on germination timing. In contrast, other genotypes showed no seed size differences across contrasting parental conditions but displayed transgenerational plasticity for germimation timing, with significantly delayed germination in saline conditions when parental plants were exposed to salinity. In genotypes that show significant transgenerational plastic germination response, we found significant coexpression networks derived from salt responsive transcripts involved in post-transcriptional regulation of the germination pathway. Consistent with the delayed germination response to saline conditions in these genotypes, we found genes associated with dormancy and up-regulation of abscisic acid (ABA). CONCLUSIONS Our results demonstrate genetic variation in transgenerational plasticity within M. truncatula and show that parental exposure to salinity stress influences the expression of stored seed transcripts, seed weight, and germination behavior. Furthermore, we show that the parental environment influences gene expression to modulate biological pathways that are likely responsible for offspring germination responses to salinity stress.
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Affiliation(s)
- Wendy T Vu
- Section of Molecular and Computational Biology, Department of Biology, University of Southern California, Los Angeles, USA.
| | - Peter L Chang
- Section of Molecular and Computational Biology, Department of Biology, University of Southern California, Los Angeles, USA.
| | - Ken S Moriuchi
- Plant Pathology, University of California at Davis, 116 Robbins Hall, Davis, CA, USA.
| | - Maren L Friesen
- Section of Molecular and Computational Biology, Department of Biology, University of Southern California, Los Angeles, USA. .,Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
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Friesen ML, von Wettberg EJB, Badri M, Moriuchi KS, Barhoumi F, Chang PL, Cuellar-Ortiz S, Cordeiro MA, Vu WT, Arraouadi S, Djébali N, Zribi K, Badri Y, Porter SS, Aouani ME, Cook DR, Strauss SY, Nuzhdin SV. The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula. BMC Genomics 2014; 15:1160. [PMID: 25534372 PMCID: PMC4410866 DOI: 10.1186/1471-2164-15-1160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress. Results Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape. Conclusions This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1160) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maren L Friesen
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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Cabot C, Sibole JV, Barceló J, Poschenrieder C. Lessons from crop plants struggling with salinity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 226:2-13. [PMID: 25113445 DOI: 10.1016/j.plantsci.2014.04.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/28/2014] [Accepted: 04/21/2014] [Indexed: 05/25/2023]
Abstract
Salinity is a persistent problem, causing important losses in irrigated agriculture. According to global climate change prediction models, salinity is expected to expand in the near future. Although intensive studies have been conducted on the mechanisms by which plants cope with saline conditions, the multi-component nature of salt stress tolerance has rendered most plant breeding efforts to improve the plant's response to salinity unsuccessful. This occurs despite the extensive genetic diversity shown by higher plants for salt tolerance and the similar mechanisms found in salt-sensitive and salt-tolerant genotypes in response to the presence of excess of salts in the growth media. On the other hand, there is an urge to increase crop yield to the maximum to cope with the growing world population demands for food and fuel. Here, we examine some major elements and signaling mechanisms involved in the plant's response to salinity following the pathway of salt-footprints from the soil environment to leaf. Some of the possible contrasting determinants for a better-balanced resource allocation between salt tolerance and plant growth and yield are considered.
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Affiliation(s)
- Catalina Cabot
- Departament de Biologia, Universitat de les Illes Balears, 07122 Palma, Illes Balears, Spain.
| | - John V Sibole
- Departament de Biologia, Universitat de les Illes Balears, 07122 Palma, Illes Balears, Spain
| | - Juan Barceló
- Lab. Fisiologia Vegetal, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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Exbrayat S, Bertoni G, Naghavie MR, Peyghambari A, Badri M, Debelle F. Genetic variability and identification of quantitative trait loci affecting plant growth and chlorophyll fluorescence parameters in the model legume Medicago truncatula under control and salt stress conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:983-1001. [PMID: 32481051 DOI: 10.1071/fp13370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/14/2014] [Indexed: 06/11/2023]
Abstract
Salinity is one of the major stresses that limits crop production worldwide and affects most physiological activities in plants. In order to study the genetic control of salt stress in the model legume Medicago truncatula Gaertn., an experiment was undertaken to determine the genetic variability and to identify quantitative trait loci (QTLs) controlling several traits related to plant growth and physiology in a population of recombinant inbred lines. Shoot and root DW, relative water content, leaf area, chlorophyll content, chlorophyll fluorescence parameters, and Na+ and K+ in shoots and roots were measured. The experiment was carried out with three replications. ANOVA showed a large genetic variation and transgressive segregation for the traits studied, suggesting putative complex tolerance mechanisms. A total of 21 QTLs were detected under control conditions and 19 QTLs were identified under 100mm salt stress conditions, with three QTLs being common to both situations. The percentage of total phenotypic variance explained by the QTLs ranged from 4.6% to 23.01%. Overlapping QTLs for different traits were also observed, which enables us to discriminate independent traits from linked ones. The results should be helpful information for further functional analysis of salt tolerance in M. truncatula.
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Affiliation(s)
- Sarah Exbrayat
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes (UMR441 and UMR 2594), 18 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Georges Bertoni
- Institut National Polytechnique (INP), Ecole Nationale Supérieure Agronomique de Toulouse (ENSAT), Unité Mixte Recherche DYNAFOR (Dynamiques et Écologie des Paysages Agriforestiers), Université de Toulouse, BP 32607, 31326 Castanet-Tolosan, France
| | - Mohamad Reza Naghavie
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Peyghambari
- Agronomy and Plant Breeding Department, Agricultural & Natural Resources College, University of Tehran, Karaj, 31587-11167, Iran
| | - Mounavar Badri
- Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Frédéric Debelle
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes (UMR441 and UMR 2594), 18 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
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Jalvingh KM, Chang PL, Nuzhdin SV, Wertheim B. Genomic changes under rapid evolution: selection for parasitoid resistance. Proc Biol Sci 2014; 281:20132303. [PMID: 24500162 PMCID: PMC3924063 DOI: 10.1098/rspb.2013.2303] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/14/2014] [Indexed: 12/30/2022] Open
Abstract
In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow 'selected regions'. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.
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Affiliation(s)
- Kirsten M. Jalvingh
- Evolutionary Genetics Group, University of Groningen, Groningen, The Netherlands
- Theoretical Biology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Peter L. Chang
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V. Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bregje Wertheim
- Evolutionary Genetics Group, University of Groningen, Groningen, The Netherlands
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16
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Cordeiro MA, Moriuchi KS, Fotinos TD, Miller KE, Nuzhdin SV, von Wettberg EJ, Cook DR. Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:488-498. [PMID: 24638163 DOI: 10.3732/ajb.1300285] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Seedling establishment and survival are highly sensitive to soil salinity and plants that evolved in saline environments are likely to express traits that increase fitness in those environments. Such traits are of ecological interest and they may have practical value for improving salt tolerance in cultivated species. We examined responses to soil salinity and tested potential mechanisms of salt tolerance in Medicago truncatula, using genotypes that originated from natural populations occurring on saline and nonsaline soils. METHODS Germination and seedling responses were quantified and compared between saline and nonsaline origin genotypes. Germination treatments included a range of sodium chloride (NaCl) concentrations in both offspring and parental environments. Seedling treatments included NaCl, abscisic acid (ABA), and potassium chloride (KCl). KEY RESULTS Saline origin genotypes displayed greater salinity tolerance for germination and seedling traits relative to nonsaline origin genotypes. We observed population specific differences for the effects of salinity on time to germination and for the impact of parental environment on germination rates. ABA and NaCl treatments had similar negative effects on root growth, although relative sensitivities differed, with saline population less sensitive to NaCl and more sensitive to ABA compared to their nonsaline counterparts. CONCLUSIONS We report population differentiation for germination and seedling growth traits under saline conditions among populations derived from saline and nonsaline environments. These observations are consistent with a syndrome of adaptations for salinity tolerance during early plant development, including traits that are common among saline environments and those that are idiosyncratic to local populations.
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Affiliation(s)
- Matilde A Cordeiro
- Department of Plant Pathology, University of California, Davis, California 95616 USA
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Gallardo K, Courty PE, Le Signor C, Wipf D, Vernoud V. Sulfate transporters in the plant's response to drought and salinity: regulation and possible functions. FRONTIERS IN PLANT SCIENCE 2014; 5:580. [PMID: 25400648 PMCID: PMC4212607 DOI: 10.3389/fpls.2014.00580] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/08/2014] [Indexed: 05/20/2023]
Abstract
Drought and salinity are two frequently combined abiotic stresses that affect plant growth, development, and crop productivity. Sulfate, and molecules derived from this anion such as glutathione, play important roles in the intrinsic responses of plants to such abiotic stresses. Therefore, understanding how plants facing environmental constraints re-equilibrate the flux of sulfate between and within different tissues might uncover perspectives for improving tolerance against abiotic stresses. In this review, we took advantage of genomics and post-genomics resources available in Arabidopsis thaliana and in the model legume species Medicago truncatula to highlight and compare the regulation of sulfate transporter genes under drought and salt stress. We also discuss their possible function in the plant's response and adaptation to abiotic stresses and present prospects about the potential benefits of mycorrhizal associations, which by facilitating sulfate uptake may assist plants to cope with abiotic stresses. Several transporters are highlighted in this review that appear promising targets for improving sulfate transport capacities of crops under fluctuating environmental conditions.
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Affiliation(s)
- Karine Gallardo
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
- *Correspondence: Karine Gallardo, Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue de Sully, BP 86510, Dijon, France e-mail:
| | - Pierre-Emmanuel Courty
- Zurich-Basel Plant Science Center, Department of Environmental Sciences, Botany, University of Basel, BaselSwitzerland
| | - Christine Le Signor
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
| | - Daniel Wipf
- Université de Bourgogne, UMR1347 Agroécologie, DijonFrance
| | - Vanessa Vernoud
- Institut National de la Recherche Agronomique, UMR1347 Agroécologie, DijonFrance
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18
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Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, Young ND, Tiffin P. Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Mol Ecol 2013; 22:3525-38. [PMID: 23773281 DOI: 10.1111/mec.12329] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/22/2013] [Accepted: 03/12/2013] [Indexed: 12/15/2022]
Abstract
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
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Affiliation(s)
- Timothy Paape
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
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Djébali N, Aribi S, Taamalli W, Arraouadi S, Aouani ME, Badri M. Natural variation of Medicago truncatula resistance to Aphanomyces euteiches. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2013; 135:831-843. [PMID: 0 DOI: 10.1007/s10658-012-0127-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Andrew RL, Kane NC, Baute GJ, Grassa CJ, Rieseberg LH. Recent nonhybrid origin of sunflower ecotypes in a novel habitat. Mol Ecol 2012; 22:799-813. [DOI: 10.1111/mec.12038] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Greg J. Baute
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Christopher J. Grassa
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
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Galeano CH, Cortés AJ, Fernández AC, Soler Á, Franco-Herrera N, Makunde G, Vanderleyden J, Blair MW. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean. BMC Genet 2012; 13:48. [PMID: 22734675 PMCID: PMC3464600 DOI: 10.1186/1471-2156-13-48] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/21/2012] [Indexed: 12/19/2022] Open
Abstract
Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.
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Affiliation(s)
- Carlos H Galeano
- Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, 3001, Heverlee, Belgium.
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Abstract
Legumes are the third-largest family of angiosperms, the second-most-important crop family, and a key source of biological nitrogen in agriculture. Recently, the genome sequences of Glycine max (soybean), Medicago truncatula, and Lotus japonicus were substantially completed. Comparisons among legume genomes reveal a key role for duplication, especially a whole-genome duplication event approximately 58 Mya that is shared by most agriculturally important legumes. A second and more recent genome duplication occurred only in the lineage leading to soybean. Outcomes of genome duplication, including gene fractionation and sub- and neofunctionalization, have played key roles in shaping legume genomes and in the evolution of legume-specific traits. Analysis of legume genome sequences also enables the discovery of legume-specific gene families and provides a framework for genome-wide association mapping that will target phenotypes of special importance in legumes. Translating genomic resources from sequenced species to less studied but still important "orphan" legumes will enhance prospects for world food production.
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Affiliation(s)
- Nevin D Young
- Department of Plant Pathology and Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA.
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Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A 2011; 108:E864-70. [PMID: 21949378 DOI: 10.1073/pnas.1104032108] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.
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