1
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Wijfjes RY, Boesten R, Becker FFM, Theeuwen TPJM, Snoek BL, Mastoraki M, Verheijen JJ, Güvencli N, Denkers LAM, Koornneef M, van Eeuwijk FA, Smit S, de de Ridder D, Aarts MGM. Allelic variants confer Arabidopsis adaptation to small regional environmental differences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39400686 DOI: 10.1111/tpj.17067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/30/2024] [Accepted: 09/19/2024] [Indexed: 10/15/2024]
Abstract
Natural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.
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Affiliation(s)
- Raúl Y Wijfjes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - René Boesten
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Tom P J M Theeuwen
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Maria Mastoraki
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Jelle J Verheijen
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Nuri Güvencli
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Lissy-Anne M Denkers
- Department of Plant Physiology, Green Life Science Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam, 1098 XH, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Dick de de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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2
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Karasov TL, Neumann M, Leventhal L, Symeonidi E, Shirsekar G, Hawks A, Monroe G, Exposito-Alonso M, Bergelson J, Weigel D, Schwab R. Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought. Nat Microbiol 2024; 9:2748-2758. [PMID: 39242816 PMCID: PMC11457713 DOI: 10.1038/s41564-024-01773-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/02/2024] [Indexed: 09/09/2024]
Abstract
Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Here, using 16S ribosomal DNA and shotgun sequencing, we characterized the associations of the Arabidopsis thaliana leaf microbiome with host genetics and climate variables from 267 populations in the species' native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in A. thaliana segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.
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Affiliation(s)
- Talia L Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Robert Bosch GmbH, Renningen, Germany
| | - Laura Leventhal
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Plant Science, Stanford, CA, USA
| | - Efthymia Symeonidi
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Entomology and Plant Pathology, Institute of Agriculture, University of Tennessee, Knoxville, TN, USA
| | - Aubrey Hawks
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Moisés Exposito-Alonso
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Plant Science, Stanford, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joy Bergelson
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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3
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Whiting JR, Booker TR, Rougeux C, Lind BM, Singh P, Lu M, Huang K, Whitlock MC, Aitken SN, Andrew RL, Borevitz JO, Bruhl JJ, Collins TL, Fischer MC, Hodgins KA, Holliday JA, Ingvarsson PK, Janes JK, Khandaker M, Koenig D, Kreiner JM, Kremer A, Lascoux M, Leroy T, Milesi P, Murray KD, Pyhäjärvi T, Rellstab C, Rieseberg LH, Roux F, Stinchcombe JR, Telford IRH, Todesco M, Tyrmi JS, Wang B, Weigel D, Willi Y, Wright SI, Zhou L, Yeaman S. The genetic architecture of repeated local adaptation to climate in distantly related plants. Nat Ecol Evol 2024; 8:1933-1947. [PMID: 39187610 PMCID: PMC11461274 DOI: 10.1038/s41559-024-02514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 07/22/2024] [Indexed: 08/28/2024]
Abstract
Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.
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Affiliation(s)
- James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Tom R Booker
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Brandon M Lind
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, Faculty of Science, University of British Columbia, Vancouver, British Colombia, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jeremy J Bruhl
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Timothy L Collins
- Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Department of Climate Change, Energy, the Environment and Water, Queanbeyan, New South Wales, Australia
| | - Martin C Fischer
- ETH Zurich: Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jasmine K Janes
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Ecosystem Science and Management, University of Northern British Columbia, Prince George, British Columbia, Canada
- Species Survival Commission, Orchid Specialist Group, IUCN North America, Washington, DC, USA
| | - Momena Khandaker
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Antoine Kremer
- UMR BIOGECO, INRAE, Université de Bordeaux; 69 Route d'Arcachon, Cestas, France
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thibault Leroy
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kevin D Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - John R Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ian R H Telford
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Jaakko S Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Baosheng Wang
- South China National Botanical Garden, Guangzhou, China
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Lecong Zhou
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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4
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Santos MA, Carromeu-Santos A, Quina AS, Antunes MA, Kristensen TN, Santos M, Matos M, Fragata I, Simões P. Experimental Evolution in a Warming World: The Omics Era. Mol Biol Evol 2024; 41:msae148. [PMID: 39034684 PMCID: PMC11331425 DOI: 10.1093/molbev/msae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions of the impacts of climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) is a highly effective tool that has been increasingly employed to elucidate the genetic basis of adaptation. The number of thermal evolve and resequence studies is rising, yet there is a dearth of efforts to integrate this new wealth of knowledge. Here, we review this literature showing how these studies have contributed to increase our understanding on the genetic basis of thermal adaptation. We identify two major trends: highly polygenic basis of thermal adaptation and general lack of consistency in candidate targets of selection between studies. These findings indicate that the adaptive responses to specific environments are rather independent. A review of the literature reveals several gaps in the existing research. Firstly, there is a paucity of studies done with organisms of diverse taxa. Secondly, there is a need to apply more dynamic and ecologically relevant thermal environments. Thirdly, there is a lack of studies that integrate genomic changes with changes in life history and behavioral traits. Addressing these issues would allow a more in-depth understanding of the relationship between genotype and phenotype. We highlight key methodological aspects that can address some of the limitations and omissions identified. These include the need for greater standardization of methodologies and the utilization of new technologies focusing on the integration of genomic and phenotypic variation in the context of thermal adaptation.
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Affiliation(s)
- Marta A Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Almada, Portugal
| | - Marta A Antunes
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Mauro Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
| | - Margarida Matos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Fragata
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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5
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Nagy DU, Thoma AE, Al-Gharaibeh M, Callaway RM, Flory SL, Frazee LJ, Hartmann M, Hensen I, Jandová K, Khasa DP, Lekberg Y, Pal RW, Samartza I, Shah MA, Sheng M, Slate M, Stein C, Tsunoda T, Rosche C. Among-population variation in drought responses is consistent across life stages but not between native and non-native ranges. THE NEW PHYTOLOGIST 2024; 243:922-935. [PMID: 38859570 DOI: 10.1111/nph.19895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Understanding how widespread species adapt to variation in abiotic conditions across their ranges is fundamental to ecology. Insight may come from studying how among-population variation (APV) in the common garden corresponds with the environmental conditions of source populations. However, there are no such studies comparing native vs non-native populations across multiple life stages. We examined APV in the performance and functional traits of 59 Conyza canadensis populations, in response to drought, across large aridity gradients in the native (North America) and non-native (Eurasia) ranges in three experiments. Our treatment (dry vs wet) was applied at the recruitment, juvenile, and adult life stages. We found contrasting patterns of APV in drought responses between the two ranges. In the native range, plant performance was less reduced by drought in populations from xeric than mesic habitats, but such relationship was not apparent for non-native populations. These range-specific patterns were consistent across the life stages. The weak adaptive responses of non-native populations indicate that they can become highly abundant even without complete local adaptation to abiotic environments and suggest that long-established invaders may still be evolving to the abiotic environment. These findings may explain lag times in invasions and raise concern about future expansions.
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Affiliation(s)
- Dávid U Nagy
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, 06108, Germany
| | - Arpad E Thoma
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, 06108, Germany
| | - Mohammad Al-Gharaibeh
- Department of Plant Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Ragan M Callaway
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - S Luke Flory
- Agronomy Department, University of Florida, Gainesville, FL, 32611, USA
| | - Lauren J Frazee
- Department of Ecology, Evolution, & Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | | | - Isabell Hensen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, 06108, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 04103, Germany
| | - Kateřina Jandová
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, CZ-12801, Czech Republic
| | - Damase P Khasa
- Centre for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Quebec, QC, G1V0A6, Canada
| | - Ylva Lekberg
- MPG Ranch Missoula, Florence, MT, 59833, USA
- Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Robert W Pal
- Department of Biological Sciences, Montana Technological University, Butte, MT, 59701, USA
| | - Ioulietta Samartza
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, 57001, Greece
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Min Sheng
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mandy Slate
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Claudia Stein
- Department of Biology and Environmental Science, Auburn University at Montgomery, Montgomery, AL, 36124, USA
| | - Tomonori Tsunoda
- Bioscience and Biotechnology, Fukui Prefectural University, Fukui, 910-1195, Japan
| | - Christoph Rosche
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, 06108, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 04103, Germany
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6
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Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
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Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
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7
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Nie X, Zhang Y, Chu S, Yu W, Liu Y, Yan B, Zhao S, Gao W, Li C, Shi X, Zheng R, Fang K, Qin L, Xing Y. New insights into the evolution and local adaptation of the genus Castanea in east Asia. HORTICULTURE RESEARCH 2024; 11:uhae147. [PMID: 38988617 PMCID: PMC11233864 DOI: 10.1093/hr/uhae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024]
Abstract
Chestnut plants (Castanea) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation. We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut (C. mollissima) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees.
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Affiliation(s)
- Xinghua Nie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shihui Chu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenjie Yu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yang Liu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Boqian Yan
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shuqing Zhao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenli Gao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Chaoxin Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueteng Shi
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruijie Zheng
- Liaoning Economic Forest Research Institute, Liaoning Academy of Agricultural Sciences, Dalian, 116000, China
| | - Kefeng Fang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
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8
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Davis GV, de Souza Moraes T, Khanapurkar S, Dromiack H, Ahmad Z, Bayer EM, Bhalerao RP, Walker SI, Bassel GW. Toward uncovering an operating system in plant organs. TRENDS IN PLANT SCIENCE 2024; 29:742-753. [PMID: 38036390 DOI: 10.1016/j.tplants.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023]
Abstract
Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell-cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.
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Affiliation(s)
- Gwendolyn V Davis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tatiana de Souza Moraes
- University of Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - Swanand Khanapurkar
- ASU-SFI Center for Biosocial Complex Systems, Arizona State University, Tempe, AZ 85287, USA; Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287, USA
| | - Hannah Dromiack
- ASU-SFI Center for Biosocial Complex Systems, Arizona State University, Tempe, AZ 85287, USA; Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287, USA
| | - Zaki Ahmad
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Emmanuelle M Bayer
- University of Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - Rishikesh P Bhalerao
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Sara I Walker
- ASU-SFI Center for Biosocial Complex Systems, Arizona State University, Tempe, AZ 85287, USA; Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287, USA; School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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9
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Denney DA, Patel P, Anderson JT. Elevated [CO 2] and temperature augment gas exchange and shift the fitness landscape in a montane forb. THE NEW PHYTOLOGIST 2024; 243:58-71. [PMID: 38655662 DOI: 10.1111/nph.19765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
Climate change is simultaneously increasing carbon dioxide concentrations ([CO2]) and temperature. These factors could interact to influence plant physiology and performance. Alternatively, increased [CO2] may offset costs associated with elevated temperatures. Furthermore, the interaction between elevated temperature and [CO2] may differentially affect populations from along an elevational gradient and disrupt local adaptation. We conducted a multifactorial growth chamber experiment to examine the interactive effects of temperature and [CO2] on fitness and ecophysiology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado. We tested whether increased [CO2] would enhance photosynthesis across accessions, and whether warmer conditions would depress the fitness of high-elevation accessions owing to steep reductions in temperature with increasing elevation in this system. Elevational clines in [CO2] are not as evident, making it challenging to predict how locally adapted ecotypes will respond to elevated [CO2]. This experiment revealed that elevated [CO2] increased photosynthesis and intrinsic water use efficiency across all accessions. However, these instantaneous responses to treatments did not translate to changes in fitness. Instead, increased temperatures reduced the probability of reproduction for all accessions. Elevated [CO2] and increased temperatures interacted to shift the adaptive landscape, favoring lower elevation accessions for the probability of survival and fecundity. Our results suggest that elevated temperatures and [CO2] associated with climate change could have severe negative consequences, especially for high-elevation populations.
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Affiliation(s)
- Derek A Denney
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Pratik Patel
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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10
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Gonzalez S, Swift J, Yaaran A, Xu J, Miller C, Illouz-Eliaz N, Nery JR, Busch W, Zait Y, Ecker JR. Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 2024; 12:RP84747. [PMID: 38904663 PMCID: PMC11192529 DOI: 10.7554/elife.84747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level. Here, we demonstrate that these different methods of lowering water potential elicit both shared and distinct transcriptional responses in Arabidopsis shoot and root tissue. When we compared these transcriptional responses to those found in Arabidopsis roots subject to vermiculite drying, we discovered many genes induced by vermiculite drying were repressed by low water potential treatments on agar plates (and vice versa). Additionally, we also tested another method for lowering water potential of agar media. By increasing the nutrient content and tensile strength of agar, we show the 'hard agar' (HA) treatment can be leveraged as a high-throughput assay to investigate natural variation in Arabidopsis growth responses to low water potential.
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Affiliation(s)
- Stephen Gonzalez
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Adi Yaaran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Jiaying Xu
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Charlotte Miller
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Natanella Illouz-Eliaz
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Wolfgang Busch
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Yotam Zait
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, The Salk Institute for Biological StudiesLa JollaUnited States
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11
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de la Mata R, Mollá-Morales A, Méndez-Vigo B, Torres-Pérez R, Oliveros JC, Gómez R, Marcer A, Castilla AR, Nordborg M, Alonso-Blanco C, Picó FX. Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity. BMC Ecol Evol 2024; 24:56. [PMID: 38702598 PMCID: PMC11067129 DOI: 10.1186/s12862-024-02246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. RESULTS Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. CONCLUSIONS Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.
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Affiliation(s)
- Raul de la Mata
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
- Faculty of Forestry, Institute of Dehesa Research (INDEHESA), Universidad de Extremadura, 10600, Plasencia, Spain
| | | | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rocío Gómez
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
| | - Arnald Marcer
- CREAF, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
| | - Antonio R Castilla
- Department of Plant Biology, Ecology, and Evolution, College of Arts and Sciences, Oklahoma State University, Stillwater, OK, 74078-3031, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain.
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12
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Wadgymar SM, Sheth S, Josephs E, DeMarche M, Anderson J. Defining fitness in evolutionary ecology. INTERNATIONAL JOURNAL OF PLANT SCIENCES 2024; 185:218-227. [PMID: 39035046 PMCID: PMC11257499 DOI: 10.1086/729360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
An understanding of biological fitness is central to theory and practice in ecology and evolution, yet fitness remains an elusive concept to define and challenging to measure accurately. Fitness reflects an individual's ability to pass its alleles on to subsequent generations. Researchers often quantify proxies for fitness, such as survival, growth or reproductive success. However, it can be difficult to determine lifetime fitness, especially for species with long lifespans. The abiotic and biotic environment strongly affects the expression of fitness, which means that fitness components can vary through both space and time. This spatial and temporal heterogeneity results in the impressive range of adaptations that we see in nature. Here, we review definitions of fitness and approaches to measuring fitness at the level of genes, individuals, genotypes, and populations and highlight that fitness is a key concept linking ecological and evolutionary thought.
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Affiliation(s)
| | - Seema Sheth
- Department of Plant and Microbial Biology, North Carolina State University
| | - Emily Josephs
- Department of Plant Biology, Michigan State University
| | | | - Jill Anderson
- Department of Genetics & Odum School of Ecology, University of Georgia
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13
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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14
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Andersson L, Bekkevold D, Berg F, Farrell ED, Felkel S, Ferreira MS, Fuentes-Pardo AP, Goodall J, Pettersson M. How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map. Annu Rev Anim Biosci 2024; 12:1-20. [PMID: 37906837 DOI: 10.1146/annurev-animal-021122-102933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Edward D Farrell
- Killybegs Fishermen's Organisation, Killybegs, County Donegal, Ireland
| | - Sabine Felkel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mafalda S Ferreira
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Angela P Fuentes-Pardo
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Jake Goodall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
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15
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Lee G, Sanderson BJ, Ellis TJ, Dilkes BP, McKay JK, Ågren J, Oakley CG. A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation. Proc Natl Acad Sci U S A 2024; 121:e2317461121. [PMID: 38289961 PMCID: PMC10861903 DOI: 10.1073/pnas.2317461121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.
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Affiliation(s)
- Gwonjin Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Brian J. Sanderson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Thomas J. Ellis
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Brian P. Dilkes
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
- Department of Biochemistry, Purdue University, West Lafayette, IN47907
| | - John K. McKay
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO80523
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
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16
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Petr M, Haller BC, Ralph PL, Racimo F. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PEER COMMUNITY JOURNAL 2023; 3:e121. [PMID: 38984034 PMCID: PMC11233137 DOI: 10.24072/pcjournal.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
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Affiliation(s)
- Martin Petr
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
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17
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Lovell RSL, Collins S, Martin SH, Pigot AL, Phillimore AB. Space-for-time substitutions in climate change ecology and evolution. Biol Rev Camb Philos Soc 2023; 98:2243-2270. [PMID: 37558208 DOI: 10.1111/brv.13004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
Abstract
In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long-term biological data to use the past to anticipate the future, spatial climate-biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space-for-time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate-focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable - population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate-biotic relationships and (ii) the transferability of these relationships, i.e. whether climate-biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields.
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Affiliation(s)
- Rebecca S L Lovell
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Sinead Collins
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Simon H Martin
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Alex L Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Albert B Phillimore
- Ashworth Laboratories, Institute of Ecology and Evolution, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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18
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Feng S, Xi E, Wan W, Ru D. Genomic signals of local adaptation in Picea crassifolia. BMC PLANT BIOLOGY 2023; 23:534. [PMID: 37919677 PMCID: PMC10623705 DOI: 10.1186/s12870-023-04539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. RESULTS Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. CONCLUSIONS Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Holzmann KL, Walls RL, Wiens JJ. Accelerating local extinction associated with very recent climate change. Ecol Lett 2023; 26:1877-1886. [PMID: 37721806 DOI: 10.1111/ele.14303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Climate change has already caused local extinction in many plants and animals, based on surveys spanning many decades. As climate change accelerates, the pace of these extinctions may also accelerate, potentially leading to large-scale, species-level extinctions. We tested this hypothesis in a montane lizard. We resurveyed 18 mountain ranges in 2021-2022 after only ~7 years. We found rates of local extinction among the fastest ever recorded, which have tripled in the past ~7 years relative to the preceding ~42 years. Further, climate change generated local extinction in ~7 years similar to that seen in other organisms over ~70 years. Yet, contrary to expectations, populations at two of the hottest sites survived. We found that genomic data helped predict which populations survived and which went extinct. Overall, we show the increasing risk to biodiversity posed by accelerating climate change and the opportunity to study its effects over surprisingly brief timescales.
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Affiliation(s)
- Kim L Holzmann
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ramona L Walls
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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20
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Montazeaud G, Helleu Q, Wuest SE, Keller L. Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana. Nat Ecol Evol 2023; 7:1878-1891. [PMID: 37749402 DOI: 10.1038/s41559-023-02189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023]
Abstract
The phenotype of an individual can be affected by the genes of its conspecifics through indirect genetic effects (IGEs). IGEs have been studied across different organisms including wild and domesticated animals and plants, but little is known about their genetic architecture. Here, in a large-scale intraspecific interaction experiment, we show that the contribution of IGEs to the biomass variation of Arabidopsis thaliana is comparable to values classically reported in animals. Moreover, we identify 11 loci explaining 85.1% of the variability in IGEs. We find that positive IGE alleles (that is, those with positive effects on neighbour biomass) occur both in relict accessions from southern Eurasia and in post-glacial colonizers from northern Scandinavia, and that they are likely to have two divergent origins: for nine loci, they evolved in the post-glacial colonizers independently from the relicts, while the two others were introgressed in the post-glacial colonizer from the relicts. Finally, we find that variation in IGEs probably reflects divergent adaptations to the contrasting environments of the edges and the centre of the native range of the species. These findings reveal a surprisingly tractable genetic basis of IGEs in A. thaliana that is shaped by the ecology and the demographic history of the species.
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Affiliation(s)
- Germain Montazeaud
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS UMR7196, INSERM U1154, Paris, France
| | - Samuel E Wuest
- Group Breeding Research, Division Plant Breeding, Agroscope, Wädenswil, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Social Evolution Unit, Chesières, Switzerland.
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21
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Hagenblad J, Aloisi K, Marum P, Öhlund L, Solberg SØ, Asdal Å, Palmé A. Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover ( Trifolium pratense). FRONTIERS IN PLANT SCIENCE 2023; 14:1233838. [PMID: 37621888 PMCID: PMC10445542 DOI: 10.3389/fpls.2023.1233838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/03/2023] [Indexed: 08/26/2023]
Abstract
Introduction In situ and ex situ conservation are the two main approaches for preserving genetic diversity. The advantages and disadvantages of the two approaches have been discussed but their genetic effects have not been fully evaluated. Methods In this study we investigate the effects of the two conservation approaches on genetic diversity in red clover. Seed samples collected from wild populations in Sweden and Norway in 1980, their subsequent generations created during seed regeneration at the gene bank and samples recollected from the same location as the original samples, were analyzed with microsatellite markers, alongside reference samples from cultivars. Results Overall, there was a differentiation between cultivars and the wild material and between wild material from Sweden and Norway. In general, the original collections clustered together with the later generations of the same accession in the gene bank, and with the recollected samples from the same location, and the level of diversity remained the same among samples of the same accession. Limited gene flow from cultivated varieties to the wild populations was detected; however, some wild individuals are likely to be escapees or affected by gene flow. Discussion In conclusion, there were examples of genetic changes within individual accessions both in situ and ex situ, as is also to be expected in any living population. However, we observed only limited genetic changes in both in situ and ex situ conservation over the generations included in this study and with the relatively large populations used in the ex situ conservation in the gene bank at NordGen.
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Affiliation(s)
- Jenny Hagenblad
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Karolina Aloisi
- Nordic Genetic Resource Center (NordGen), Alnarp, Sweden
- Malmö University, Malmö, Sweden
| | | | | | - Svein Øivind Solberg
- Department of Agricultural Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, Elverum, Norway
| | - Åsmund Asdal
- Nordic Genetic Resource Center (NordGen), Alnarp, Sweden
| | - Anna Palmé
- Nordic Genetic Resource Center (NordGen), Alnarp, Sweden
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22
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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23
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Hesen V, Boele Y, Bakx-Schotman T, van Beersum F, Raaijmakers C, Scheres B, Willemsen V, van der Putten WH. Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:62. [PMID: 37468998 DOI: 10.1186/s40793-023-00511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome. RESULTS We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in. CONCLUSIONS Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
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Affiliation(s)
- Vera Hesen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
| | - Yvet Boele
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Tanja Bakx-Schotman
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Femke van Beersum
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
- Plant Ecology and Nature Conservation Group, Wageningen University, Droevendaalsesteeg 3a, Wageningen, 6708 PB, the Netherlands
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS, the Netherlands
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
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Abstract
Photoperiod-measuring mechanisms allow organisms to anticipate seasonal changes to align reproduction and growth with appropriate times of the year. This review provides historical and modern context to studies of plant photoperiodism. We describe how studies of photoperiodic flowering in plants led to the first theoretical models of photoperiod-measuring mechanisms in any organism. We discuss how more recent molecular genetic studies in Arabidopsis and rice have revisited these concepts. We then discuss how photoperiod transcriptomics provides new lessons about photoperiodic gene regulatory networks and the discovery of noncanonical photoperiod-measuring systems housed in metabolic networks of plants. This leads to an examination of nonflowering developmental processes controlled by photoperiod, including metabolism and growth. Finally, we highlight the importance of understanding photoperiodism in the context of climate change, delving into the rapid latitudinal migration of plant species and the potential role of photoperiod-measuring systems in generating photic barriers during migration.
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Affiliation(s)
- Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA;
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany;
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25
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Schlötterer C. How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220046. [PMID: 37004724 PMCID: PMC10067264 DOI: 10.1098/rstb.2022.0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Experimental evolution is well-suited to test the predictability of evolution without the confounding effects of inaccurate forecasts about future environments. Most of the literature about parallel (and thus predictable) evolution has been carried out in asexual microorganisms, which adapt by de novo mutations. Nevertheless, parallel evolution has also been studied in sexual species at the genomic level. Here, I review the evidence for parallel evolution in Drosophila, the best-studied obligatory outcrossing model for adaptation from standing genetic variation in the laboratory. Similar to asexual microorganisms, evidence for parallel evolution varies between the focal hierarchical levels. Selected phenotypes consistently respond in a very predicable way, but the underlying allele frequency changes are much less predictable. The most important insight is that the predictability of the genomic selection response for polygenic traits depends highly on the founder population and to a much lesser extent on the selection regime. This implies that predicting adaptive genomic response is challenging and requires a good understanding of the adaptive architecture (including linkage disequilibrium) in the ancestral populations. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
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26
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Reis RS. Thermomorphogenesis: Opportunities and challenges in posttranscriptional regulation. JOURNAL OF EXPERIMENTAL BOTANY 2023:7134107. [PMID: 37082809 DOI: 10.1093/jxb/erad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 05/03/2023]
Abstract
Plants exposed to mildly elevated temperatures display morphological and developmental changes collectively termed thermomorphogenesis. This adaptative process has several undesirable consequences to food production, including yield reduction and increased vulnerability to pathogens. Understanding thermomorphogenesis is, thus, critical for understanding how plants will respond to increasingly warmer temperature conditions, such as those caused by climate change. Recently, we have made major advances in that direction, and it has become apparent that plants resource to a broad range of molecules and molecular mechanisms to perceive and respond to increases in environmental temperature. However, most of our efforts have been focused on regulation of transcription and protein abundance and activity, with an important gap encompassing nearly all processes involving RNA (i.e., posttranscriptional regulation). Here, I summarized our current knowledge of thermomorphogenesis involving transcriptional, posttranscriptional, and posttranslational regulation, focused on opportunities and challenges in understanding posttranscriptional regulation-a fertile field for exciting new discoveries.
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Affiliation(s)
- Rodrigo S Reis
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
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27
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Sobral M. Induction of subindividual variation: a commentary on 'Intra-individual variation in Galium odoratum is affected by experimental drought and shading'. ANNALS OF BOTANY 2023; 131:i-ii. [PMID: 36806383 PMCID: PMC10072083 DOI: 10.1093/aob/mcad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Mar Sobral
- CRETUS – EcoPast (GI-1553), Departmento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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28
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Torres E, García-Fernández A, Iñigo D, Lara-Romero C, Morente-López J, Prieto-Benítez S, Rubio Teso ML, Iriondo JM. Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide. PLANTS (BASEL, SWITZERLAND) 2023; 12:1258. [PMID: 36986946 PMCID: PMC10053585 DOI: 10.3390/plants12061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.
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Affiliation(s)
- Elena Torres
- Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Alfredo García-Fernández
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Diana Iñigo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Carlos Lara-Romero
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Javier Morente-López
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Grupo de Investigación de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 Tenerife, Spain
| | - Samuel Prieto-Benítez
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
- Ecotoxicology of Air Pollution, Environmental Department, CIEMAT, 28040 Madrid, Spain
| | - María Luisa Rubio Teso
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - José M. Iriondo
- Grupo de Ecología Evolutiva (ECOEVO), Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
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29
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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30
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Exposito-Alonso M. Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology. THE NEW PHYTOLOGIST 2023; 237:2005-2011. [PMID: 36604850 DOI: 10.1111/nph.18718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because different populations may be more or less susceptible to global change and, if lost, would reduce the total diversity within a species. Two new modeling frameworks advance our understanding of extinction from a population and evolutionary angle: Rapid climate change-driven disruptions in population adaptation are predicted from associations between genomes and local climates. Furthermore, losses of population diversity from global land-use transformations are estimated by scaling relationships of species' genomic diversity with habitat area. Overall, these global eco-evolutionary methods advance the predictability - and possibly the preventability - of the ongoing extinction of plant species.
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Affiliation(s)
- Moi Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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31
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Marszalek-Zenczak M, Satyr A, Wojciechowski P, Zenczak M, Sobieszczanska P, Brzezinski K, Iefimenko T, Figlerowicz M, Zmienko A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. FRONTIERS IN PLANT SCIENCE 2023; 14:1104303. [PMID: 36778696 PMCID: PMC9909608 DOI: 10.3389/fpls.2023.1104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
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Affiliation(s)
| | - Anastasiia Satyr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tetiana Iefimenko
- Department of Biology, National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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32
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Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata. Commun Biol 2023; 6:5. [PMID: 36596992 PMCID: PMC9810668 DOI: 10.1038/s42003-022-04407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
The roles of synonymous mutations for adapting to stressful thermal environments are of fundamental biological and ecological interests but poorly understood. To study whether synonymous mutations influence thermal adaptation at specific microhabitats, a genome-wide genotype-phenotype association analysis is carried out in the black mussels Mytilisepta virgata. A synonymous mutation of Ubiquitin-specific Peptidase 15 (MvUSP15) is significantly associated with the physiological upper thermal limit. The individuals carrying GG genotype (the G-type) at the mutant locus possess significantly lower heat tolerance compared to the individuals carrying GA and AA genotypes (the A-type). When heated to sublethal temperature, the G-type exhibit higher inter-individual variations in MvUSP15 expression, especially for the mussels on the sun-exposed microhabitats. Taken together, a synonymous mutation in MvUSP15 can affect the gene expression profile and interact with microhabitat heterogeneity to influence thermal resistance. This integrative study sheds light on the ecological importance of adaptive synonymous mutations as an underappreciated genetic buffer against heat stress and emphasizes the importance of integrative studies at a microhabitat scale for evaluating and predicting the impacts of climate change.
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33
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. THE PLANT CELL 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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34
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Wang Y, Zhang L, Zhou Y, Ma W, Li M, Guo P, Feng L, Fu C. Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China. Front Genet 2023; 14:1150704. [PMID: 37144128 PMCID: PMC10151583 DOI: 10.3389/fgene.2023.1150704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.
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Affiliation(s)
- Yihan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Lin Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Yuchao Zhou
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Wenxin Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Manyu Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
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35
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Negin B, Aharoni A. Let's connect nature with hypothesis-based experimentation and explore life in context. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:23-25. [PMID: 36423223 DOI: 10.1111/tpj.16030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
In a recent paper in Nature, Edith Heard from the European Molecular Biology Laboratory (EMBL) suggested that molecular biologists should 'reconnect with nature' by diversifying sampling locations. Although this approach has its own benefits, we suggest that advanced methods should rather be used to take hypothesis-based experiments to nature, thereby supplying a much-needed context for experimentation under controlled conditions. Following the CRISPR (clustered regularly interspaced short palindromic repeats) revolution, this approach has become accessible to many research groups. For the past several years we have developed the groundwork and initiated such experimentation. This included the assembly of a mobile laboratory on a four-wheel drive truck and examining genome-edited metabolic mutants in wild tree tobacco (Nicotiana glauca), grown in nature. Our findings included both targeted answers to focused questions, but also surprising results that could only be reached while working in natural settings.
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Affiliation(s)
- Boaz Negin
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
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36
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Kreiner JM, Latorre SM, Burbano HA, Stinchcombe JR, Otto SP, Weigel D, Wright SI. Rapid weed adaptation and range expansion in response to agriculture over the past two centuries. Science 2022; 378:1079-1085. [PMID: 36480621 DOI: 10.1126/science.abo7293] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century.
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Affiliation(s)
- Julia M Kreiner
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sarah P Otto
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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37
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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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38
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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39
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Feng T, Wu P, Gao H, Kosma DK, Jenks MA, Lü S. Natural variation in root suberization is associated with local environment in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:385-398. [PMID: 35751382 DOI: 10.1111/nph.18341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Genetic signature of climate adaptation has been widely recognized across the genome of many organisms; however, the eco-physiological basis for linking genomic polymorphisms with local adaptations remains largely unexplored. Using a panel of 218 world-wide Arabidopsis accessions, we characterized the natural variation in root suberization by quantifying 16 suberin monomers. We explored the associations between suberization traits and 126 climate variables. We conducted genome-wide association analysis and integrated previous genotype-environment association (GEA) to identify the genetic bases underlying suberization variation and their involvements in climate adaptation. Root suberin content displays extensive variation across Arabidopsis populations and significantly correlates with local moisture gradients and soil characteristics. Specifically, enhanced suberization is associated with drier environments, higher soil cation-exchange capacity, and lower soil pH; higher proportional levels of very-long-chain suberin is negatively correlated with moisture availability, lower soil gravel content, and higher soil silt fraction. We identified 94 putative causal loci and experimentally proved that GPAT6 is involved in C16 suberin biosynthesis. Highly significant associations between the putative genes and environmental variables were observed. Roots appear highly responsive to environmental heterogeneity via regulation of suberization, especially the suberin composition. The patterns of suberization-environment correlation and the suberin-related GEA fit the expectations of local adaptation for the polygenic suberization trait.
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Affiliation(s)
- Tao Feng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Pan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Huani Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Matthew A Jenks
- School of Plant Sciences, College of Agriculture and Life Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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40
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Thieme M, Brêchet A, Bourgeois Y, Keller B, Bucher E, Roulin AC. Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:182-194. [PMID: 35715973 PMCID: PMC9544478 DOI: 10.1111/nph.18322] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/10/2022] [Indexed: 05/14/2023]
Abstract
Eukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognised as a source of genetic diversity and powerful drivers of evolution. However, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scarce. We exposed Arabidopsis thaliana high-copy TE lines (hcLines) with up to c. eight-fold increased copy numbers of the heat-responsive ONSEN TE to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis, plant size and water consumption. Overall, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in A. thaliana. This is one of the rare empirical examples substantiating the adaptive potential of mobilised stress-responsive TEs in eukaryotes. Our work demonstrates the potential of TE-mediated loss-of-function mutations in stress adaptation.
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Affiliation(s)
- Michael Thieme
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
| | - Arthur Brêchet
- Department of Environmental Sciences – BotanyUniversity of Basel4056BaselSwitzerland
| | - Yann Bourgeois
- School of Biological SciencesUniversity of PortsmouthPO1 2DTPortsmouthUK
| | - Bettina Keller
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
| | | | - Anne C. Roulin
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
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41
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Exposito-Alonso M, Booker TR, Czech L, Gillespie L, Hateley S, Kyriazis CC, Lang PLM, Leventhal L, Nogues-Bravo D, Pagowski V, Ruffley M, Spence JP, Toro Arana SE, Weiß CL, Zess E. Genetic diversity loss in the Anthropocene. Science 2022; 377:1431-1435. [PMID: 36137047 DOI: 10.1126/science.abn5642] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Anthropogenic habitat loss and climate change are reducing species' geographic ranges, increasing extinction risk and losses of species' genetic diversity. Although preserving genetic diversity is key to maintaining species' adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations' post-2020 targets for genetic preservation.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Lauren Gillespie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Laura Leventhal
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Nogues-Bravo
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Megan Ruffley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Jeffrey P Spence
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sebastian E Toro Arana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin Zess
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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42
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Ruiz-Diaz MJ, Matsusaka D, Cascales J, Sánchez DH, Sánchez-Lamas M, Cerdán PD, Botto JF. Functional analysis of PHYB polymorphisms in Arabidopsis thaliana collected in Patagonia. FRONTIERS IN PLANT SCIENCE 2022; 13:952214. [PMID: 36161012 PMCID: PMC9490419 DOI: 10.3389/fpls.2022.952214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana shows a wide range of natural genetic variation in light responses. Shade avoidance syndrome is a strategy of major adaptive significance that includes seed germination, elongation of vegetative structures, leaf hyponasty, and acceleration of flowering. Previously, we found that the southernmost Arabidopsis accession, collected in the south of Patagonia (Pat), is hyposensitive to light and displays a reduced response to shade light. This work aimed to explore the genetic basis of the shade avoidance response (SAR) for hypocotyl growth by QTL mapping in a recently developed 162 RIL population between Col-0 and Pat. We mapped four QTL for seedling hypocotyl growth: WL1 and WL2 QTL in white light, SHADE1 QTL in shade light, and SAR1 QTL for the SAR. PHYB is the strongest candidate gene for SAR1 QTL. Here we studied the function of two polymorphic indels in the promoter region, a GGGR deletion, and three non-synonymous polymorphisms on the PHYB coding region compared with the Col-0 reference genome. To decipher the contribution and relevance of each PHYB-Pat polymorphism, we constructed transgenic lines with single or double polymorphisms by using Col-0 as a reference genome. We found that single polymorphisms in the coding region of PHYB have discrete functions in seed germination, seedling development, and shade avoidance response. These results suggest distinct functions for each PHYB polymorphism to the adjustment of plant development to variable light conditions.
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Affiliation(s)
- María Jimena Ruiz-Diaz
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Matsusaka
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena Cascales
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego H. Sánchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Javier F. Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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Gramlich S, Liu X, Favre A, Buerkle CA, Karrenberg S. A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene. THE NEW PHYTOLOGIST 2022; 235:1641-1652. [PMID: 35586969 PMCID: PMC9544174 DOI: 10.1111/nph.18260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/04/2022] [Indexed: 05/27/2023]
Abstract
Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.
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Affiliation(s)
- Susanne Gramlich
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
| | - Xiaodong Liu
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
- Department of Biology, The Bioinformatics CenterUniversity of CopenhagenOle Maaløes Vej 52200CopenhagenDenmark
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumSenckenberganlage 2560325Frankfurt/MainGermany
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University AveLaramieWY82071USA
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
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Grummer JA, Booker TR, Matthey-Doret R, Nietlisbach P, Thomaz AT, Whitlock MC. The immediate costs and long-term benefits of assisted gene flow in large populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13911. [PMID: 35390208 DOI: 10.1111/cobi.13911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/11/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
With the genetic health of many plant and animal populations deteriorating due to climate change outpacing adaptation, interventions, such as assisted gene flow (AGF), may provide genetic variation necessary for populations to adapt to climate change. We ran genetic simulations to mimic different AGF scenarios in large populations and measured their outcomes on population-level fitness to determine circumstances in which it is worthwhile to perform AGF. In the absence of inbreeding depression, AGF was beneficial within a few generations only when introduced genotypes had much higher fitness than local individuals and traits affecting fitness were controlled by a few genes of large effect. AGF was harmful over short periods (e.g., first ∼10-20 generations) if there was strong outbreeding depression or introduced deleterious genetic variation. When the adaptive trait was controlled by many loci of small effect, the benefits of AGF took over 10 generations to realize-potentially too long for most climate-related management scenarios. The genomic integrity of the recipient population typically remained intact following AGF; the amount of genetic material from the donor population usually constituted no more of the recipient population's genome than the fraction of the population introduced. Significant genomic turnover (e.g., >50% replacement) only occurred when the selective advantage of the adaptive trait and translocation fraction were extremely high. Our results will be useful when adaptive management is used to maintain the genetic health and productivity of large populations under climate change.
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Affiliation(s)
- Jared A Grummer
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom R Booker
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Remi Matthey-Doret
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Pirmin Nietlisbach
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Andréa T Thomaz
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Michael C Whitlock
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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45
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Gompert Z, Feder JL, Nosil P. The short-term, genome-wide effects of indirect selection deserve study: A response to Charlesworth and Jensen (2022). Mol Ecol 2022; 31:4444-4450. [PMID: 35909250 DOI: 10.1111/mec.16614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
We recently published a paper quantifying the genome-wide consequences of natural selection, including the effects of indirect selection due to the correlation of genetic regions (neutral or selected) with directly selected regions (Gompert et al., 2022). In their critique of our paper, Charlesworth and Jensen (2022) make two main points: (i) indirect selection is equivalent to hitchhiking and thus well documented (i.e., our results are not novel) and (ii) that we do not demonstrate the source of linkage disequilibrium (LD) between SNPs and the Mel-Stripe locus in the Timema cristinae experiment we analyse. As we discuss in detail below, neither of these are substantial criticisms of our work.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, University Montpellier, CNRS, EPHE, IRD, University Paul Valéry Montpellier 3, Montpellier, France
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46
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Stern DB, Anderson NW, Diaz JA, Lee CE. Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. Nat Commun 2022; 13:4024. [PMID: 35821220 PMCID: PMC9276764 DOI: 10.1038/s41467-022-31622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
The role of epistasis in driving adaptation has remained an unresolved problem dating back to the Evolutionary Synthesis. In particular, whether epistatic interactions among genes could promote parallel evolution remains unexplored. To address this problem, we employ an Evolve and Resequence (E&R) experiment, using the copepod Eurytemora affinis, to elucidate the evolutionary genomic response to rapid salinity decline. Rapid declines in coastal salinity at high latitudes are a predicted consequence of global climate change. Based on time-resolved pooled whole-genome sequencing, we uncover a remarkably parallel, polygenic response across ten replicate selection lines, with 79.4% of selected alleles shared between lines by the tenth generation of natural selection. Using extensive computer simulations of our experiment conditions, we find that this polygenic parallelism is consistent with positive synergistic epistasis among alleles, far more so than other mechanisms tested. Our study provides experimental and theoretical support for a novel mechanism promoting repeatable polygenic adaptation, a phenomenon that may be common for selection on complex physiological traits.
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Affiliation(s)
- David B Stern
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA.
- National Biodefense Analysis and Countermeasures Center (NBACC), Operated by Battelle National Biodefense Institute (BNBI) for the U.S. Department of Homeland Security Science and Technology Directorate, Fort Detrick, MD, 21702, USA.
| | - Nathan W Anderson
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA
| | - Juanita A Diaz
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA
| | - Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA.
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47
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Morente‐López J, Kass JM, Lara‐Romero C, Serra‐Diaz JM, Soto‐Correa JC, Anderson RP, Iriondo JM. Linking ecological niche models and common garden experiments to predict phenotypic differentiation in stressful environments: Assessing the adaptive value of marginal populations in an alpine plant. GLOBAL CHANGE BIOLOGY 2022; 28:4143-4162. [PMID: 35359032 PMCID: PMC9325479 DOI: 10.1111/gcb.16181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/25/2022] [Accepted: 03/08/2022] [Indexed: 05/10/2023]
Abstract
Environmental variation within a species' range can create contrasting selective pressures, leading to divergent selection and novel adaptations. The conservation value of populations inhabiting environmentally marginal areas remains in debate and is closely related to the adaptive potential in changing environments. Strong selection caused by stressful conditions may generate novel adaptations, conferring these populations distinct evolutionary potential and high conservation value under climate change. On the other hand, environmentally marginal populations may be genetically depauperate, with little potential for new adaptations to emerge. Here, we explored the use of ecological niche models (ENMs) linked with common garden experiments to predict and test for genetically determined phenotypic differentiation related to contrasting environmental conditions. To do so, we built an ENM for the alpine plant Silene ciliata in central Spain and conducted common garden experiments, assessing flowering phenology changes and differences in leaf cell resistance to extreme temperatures. The suitability patterns and response curves of the ENM led to the predictions that: (1) the environmentally marginal populations experiencing less snowpack and higher minimum temperatures would have delayed flowering to avoid risks of late-spring frosts and (2) those with higher minimum temperatures and greater potential evapotranspiration would show enhanced cell resistance to high temperatures to deal with physiological stress related to desiccation and heat. The common garden experiments revealed the expected genetically based phenotypic differentiation in flowering phenology. In contrast, they did not show the expected differentiation for cell resistance, but these latter experiments had high variance and hence lower statistical power. The results highlight ENMs as useful tools to identify contrasting putative selective pressures across species ranges. Linking ENMs with common garden experiments provides a theoretically justified and practical way to study adaptive processes, including insights regarding the conservation value of populations inhabiting environmentally marginal areas under ongoing climate change.
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Affiliation(s)
- Javier Morente‐López
- Área de Biodiversidad y ConservaciónDepto. de Biología, GeologíaFísica y Química InorgánicaESCETUniversidad Rey Juan Carlos (URJC)MadridMóstolesSpain
- Island Ecology and Evolution Research GroupInstitute of Natural Products and Agrobiology, Consejo Superior de Investigaciones Científicas (IPNA‐CSIC)San Cristóbal de La Laguna, TenerifeSpain
| | - Jamie M. Kass
- Department of BiologyCity College of New YorkCity University of New YorkNew YorkNew YorkUSA
- Ph.D. Program in BiologyGraduate CenterCity University of New YorkNew YorkNew YorkUSA
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityKunigami‐gunOkinawaJapan
| | - Carlos Lara‐Romero
- Área de Biodiversidad y ConservaciónDepto. de Biología, GeologíaFísica y Química InorgánicaESCETUniversidad Rey Juan Carlos (URJC)MadridMóstolesSpain
| | | | - José Carmen Soto‐Correa
- Facultad de Ciencias NaturalesUniversidad Autónoma de Querétaro (FCN‐UAQ)Santa Rosa Jáuregui, QuerétaroMexico
| | - Robert P. Anderson
- Department of BiologyCity College of New YorkCity University of New YorkNew YorkNew YorkUSA
- Ph.D. Program in BiologyGraduate CenterCity University of New YorkNew YorkNew YorkUSA
- Division of Vertebrate Zoology (Mammalogy)American Museum of Natural HistoryNew YorkNew YorkUSA
| | - José M. Iriondo
- Área de Biodiversidad y ConservaciónDepto. de Biología, GeologíaFísica y Química InorgánicaESCETUniversidad Rey Juan Carlos (URJC)MadridMóstolesSpain
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48
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Siqueira JA, Wakin T, Batista-Silva W, Silva JCF, Vicente MH, Silva JC, Clarindo WR, Zsögön A, Peres LEP, De Veylder L, Fernie AR, Nunes-Nesi A, Araújo WL. A long and stressful day: Photoperiod shapes aluminium tolerance in plants. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128704. [PMID: 35313159 DOI: 10.1016/j.jhazmat.2022.128704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Aluminium (Al), a limiting factor for crop productivity in acidic soils (pH ≤ 5.5), imposes drastic constraints for food safety in developing countries. The major mechanisms that allow plants to cope with Al involve manipulations of organic acids metabolism and DNA-checkpoints. When assumed individually both approaches have been insufficient to overcome Al toxicity. On analysing the centre of origin of most cultivated plants, we hypothesised that day-length seems to be a pivotal agent modulating Al tolerance across distinct plant species. We observed that with increasing distance from the Equator, Al tolerance decreases, suggesting a relationship with the photoperiod. We verified that long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth habit boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. Furthermore, DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting that photoperiod act as a selective barrier for Al tolerance. A diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. Altogether, photoperiodic control of Al tolerance might contribute to solving the historical obstacle that imposes barriers for developing countries to reach a sustainable agriculture.
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Affiliation(s)
- João Antonio Siqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Thiago Wakin
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Matheus H Vicente
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Jéssica C Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wellington R Clarindo
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Lazaro E P Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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49
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Vasseur F, Cornet D, Beurier G, Messier J, Rouan L, Bresson J, Ecarnot M, Stahl M, Heumos S, Gérard M, Reijnen H, Tillard P, Lacombe B, Emanuel A, Floret J, Estarague A, Przybylska S, Sartori K, Gillespie LM, Baron E, Kazakou E, Vile D, Violle C. A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2022; 13:836488. [PMID: 35668791 PMCID: PMC9163986 DOI: 10.3389/fpls.2022.836488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 05/31/2023]
Abstract
The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.
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Affiliation(s)
| | - Denis Cornet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Grégory Beurier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Julie Messier
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Justine Bresson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mark Stahl
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Quantitative Biology Center (QBiC), University of Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Marianne Gérard
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hans Reijnen
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pascal Tillard
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Amélie Emanuel
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Justine Floret
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kevin Sartori
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Etienne Baron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Elena Kazakou
- CEFE, Univ Montpellier, CNRS, EPHE, Institut Agro, IRD, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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50
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Fournier-Level A, Taylor MA, Paril JF, Martínez-Berdeja A, Stitzer MC, Cooper MD, Roe JL, Wilczek AM, Schmitt J. Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 234:719-734. [PMID: 35090191 DOI: 10.1111/nph.17999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.
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Affiliation(s)
| | - Mark A Taylor
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Jefferson F Paril
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | | | - Michelle C Stitzer
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Martha D Cooper
- Department of Ecology and Evolution, Brown University, Providence, RI, 02912, USA
| | - Judith L Roe
- College of Arts and Sciences, Biology, Agricultural Science & Agribusiness, University of Maine at Presque Isle, Presque Isle, ME, 04769, USA
| | | | - Johanna Schmitt
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
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