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Nzepang DT, Gully D, Nguepjop JR, Zaiya Zazou A, Tossim HA, Sambou A, Rami JF, Hocher V, Fall S, Svistoonoff S, Fonceka D. Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors. Genes (Basel) 2023; 14:genes14040797. [PMID: 37107555 PMCID: PMC10138160 DOI: 10.3390/genes14040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis)4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs.
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Affiliation(s)
- Darius T. Nzepang
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Djamel Gully
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Joël R. Nguepjop
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Arlette Zaiya Zazou
- Institute of Agricultural Research for Development (IRAD) (IRAD), Maroua, Cameroon
| | - Hodo-Abalo Tossim
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Valerie Hocher
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Saliou Fall
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Sergio Svistoonoff
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Daniel Fonceka
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Correspondence:
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2
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Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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3
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Keeler AM, Rafferty NE. Legume germination is delayed in dry soils and in sterile soils devoid of microbial mutualists: Species-specific implications for upward range expansions. Ecol Evol 2022; 12:e9186. [PMID: 36016820 PMCID: PMC9398887 DOI: 10.1002/ece3.9186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/27/2022] [Accepted: 07/15/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is affecting species and their mutualists and can lead to the weakening or loss of important interspecific interactions. Through independent shifts in partner phenology and distribution, climatic stress can separate mutualists temporally or spatially, leading to alterations in partner functional traits and fitness. Here, we explored the effects of the loss of microbial mutualists on legume germination success and phenology. In particular, we assessed the effects of mutualism loss via soil sterilization, increased drought, and introduction to novel soils found beyond the current distributions of two focal legume species in subalpine environments. Through common garden experiments in controlled environments, we found evidence that soil sterilization (and consequent microbial absence) and dry soils caused species‐specific phenological delays of 2–5 weeks in germination, likely as a result of interaction loss between legumes and specialized germination‐promoting soil microbes, such as mutualistic rhizobia. Delays in germination caused by a mismatch between legumes and beneficial microbes could negatively affect legume fitness through increased plant–plant competition later in the season. Additionally, we found evidence of the presence of beneficial microbes beyond the current elevational range of one of our focal legumes, which may allow for expansion of the leading edge, although harsh abiotic factors in the alpine may hinder this. Alterations in the strength of soil microbe‐legume mutualisms may lead to reduced fitness and altered demography for both soil microbes and legumes.
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Affiliation(s)
- Andrea M Keeler
- Department of Evolution, Ecology, and Organismal Biology University of California, Riverside Riverside California USA.,Rocky Mountain Biological Laboratory Crested Butte Colorado USA
| | - Nicole E Rafferty
- Department of Evolution, Ecology, and Organismal Biology University of California, Riverside Riverside California USA.,Rocky Mountain Biological Laboratory Crested Butte Colorado USA
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4
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Markalanda SH, McFadden CJ, Cassidy ST, Wood CW. The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field. Ecol Evol 2022; 12:e8283. [PMID: 35126998 PMCID: PMC8796929 DOI: 10.1002/ece3.8283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/20/2021] [Accepted: 09/30/2021] [Indexed: 11/07/2022] Open
Abstract
Evidence is accumulating that the soil microbiome-the community of microorganisms living in soils-has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural plant populations. To address this gap, we performed a field experiment using the black medick Medicago lupulina to test how the soil microbiome influences plant performance and colonization by two root endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and the parasitic root-knot nematode Meloidogyne hapla) under natural conditions. We inoculated all plants with nitrogen-fixing bacteria and factorially manipulated the soil microbiome and nematode infection. We found that plants grown in microbe-depleted soil exhibit greater mortality, but that among the survivors, there was no effect of the soil microbiome on plant performance (shoot biomass, root biomass, or shoot-to-root ratio). The soil microbiome also impacted parasitic nematode infection and affected colonization by mutualistic nitrogen-fixing bacteria in a plant genotype-dependent manner, increasing colonization in some plant genotypes and decreasing it in others. Our results demonstrate the soil microbiome has complex effects on plant-endosymbiont interactions and may be critical for survival under natural conditions.
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Affiliation(s)
| | - Connor J. McFadden
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Steven T. Cassidy
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
- Present address:
Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | - Corlett W. Wood
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
- Present address:
Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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5
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From the ground up: Building predictions for how climate change will affect belowground mutualisms, floral traits, and bee behavior. CLIMATE CHANGE ECOLOGY 2021. [DOI: 10.1016/j.ecochg.2021.100013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Wendlandt CE, Helliwell E, Roberts M, Nguyen KT, Friesen ML, von Wettberg E, Price P, Griffitts JS, Porter SS. Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism. Evolution 2021; 75:731-747. [PMID: 33433925 DOI: 10.1111/evo.14164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which have coinvaded North America. We find that mutualism benefits for plants are indistinguishable between invaded- and native-range symbioses. However, rhizobia gain greater fitness from invaded-range mutualisms than from native-range mutualisms, and this enhancement of symbiont fecundity could increase the mutualism's spread by increasing symbiont availability during plant colonization. Furthermore, mutualism traits in invaded-range symbioses show lower genetic variance and a simpler partitioning of genetic variance between host and symbiont sources, compared to native-range symbioses. This suggests that biological invasion has reduced mutualists' potential to respond to coevolutionary selection. Additionally, rhizobia bearing a locus (hrrP) that can enhance symbiotic fitness have more exploitative phenotypes in invaded-range than in native-range symbioses. These findings highlight the impacts of biological invasion on the evolution of mutualistic interactions.
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Affiliation(s)
- Camille E Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Emily Helliwell
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Kyle T Nguyen
- School of Biological Sciences, Washington State University, Vancouver, Washington
| | - Maren L Friesen
- Department of Plant Pathology, Department of Crop and Soil Sciences, Washington State University, Pullman, Washington
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for the Environment, University of Vermont, Burlington, Vermont
| | - Paul Price
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, Washington
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7
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Batstone RT, O’Brien AM, Harrison TL, Frederickson ME. Experimental evolution makes microbes more cooperative with their local host genotype. Science 2020; 370:476-478. [DOI: 10.1126/science.abb7222] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rebecca T. Batstone
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Anna M. O’Brien
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Department of Mechanical & Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Tia L. Harrison
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Megan E. Frederickson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON M5S 3B2, Canada
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
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8
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Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
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Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
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9
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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10
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Cassidy ST, Burr AA, Reeb RA, Melero Pardo AL, Woods KD, Wood CW. Using clear plastic CD cases as low-cost mini-rhizotrons to phenotype root traits. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11340. [PMID: 32351801 PMCID: PMC7186896 DOI: 10.1002/aps3.11340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/03/2019] [Indexed: 06/11/2023]
Abstract
PREMISE We developed a novel low-cost method to visually phenotype belowground structures in the plant rhizosphere. We devised the method introduced here to address the difficulties encountered growing plants in seed germination pouches for long-term experiments and the high cost of other mini-rhizotron alternatives. METHODS AND RESULTS The method described here took inspiration from homemade ant farms commonly used as an educational tool in elementary schools. Using compact disc (CD) cases, we developed mini-rhizotrons for use in the field and laboratory using the burclover Medicago lupulina. CONCLUSIONS Our method combines the benefits of pots and germination pouches. In CD mini-rhizotrons, plants grew significantly larger than in germination pouches, and unlike pots, it is possible to measure roots without destructive sampling. Our protocol is a cheaper, widely available alternative to more destructive methods, which could facilitate the study of belowground phenotypes and processes by scientists with fewer resources.
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Affiliation(s)
- Steven T Cassidy
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
- Present address: Department of Biology University of Florida Gainesville Florida USA
| | - Audrey A Burr
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Rachel A Reeb
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Ana L Melero Pardo
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Kamron D Woods
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Corlett W Wood
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
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11
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Batstone RT, Peters MAE, Simonsen AK, Stinchcombe JR, Frederickson ME. Environmental variation impacts trait expression and selection in the legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2020; 107:195-208. [PMID: 32064599 DOI: 10.1002/ajb2.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/04/2019] [Indexed: 05/22/2023]
Abstract
PREMISE The ecological outcomes of mutualism are well known to shift across abiotic or biotic environments, but few studies have addressed how different environments impact evolutionary responses, including the intensity of selection on and the expression of genetic variance in key mutualism-related traits. METHODS We planted 30 maternal lines of the legume Medicago lupulina in four field common gardens and compared our measures of selection on and genetic variance in nodulation, a key trait reflecting legume investment in the symbiosis, with those from a previous greenhouse experiment using the same 30 M. lupulina lines. RESULTS We found that both the mean and genetic variance for nodulation were much greater in the greenhouse than in the field and that the form of selection on nodulation significantly differed across environments. We also found significant genotype-by-environment (G × E) effects for fitness-related traits that were generated by differences in the rank order of plant lines among environments. CONCLUSIONS Overall, our results suggest that the expression of genotypic variation and selection on nodulation differ across environments. In the field, significant rank-order changes for plant fitness potentially help maintain genetic variation in natural populations, even in the face of directional or stabilizing selection.
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Affiliation(s)
- Rebecca T Batstone
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Carl Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL, 61801, USA
| | - Madeline A E Peters
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Anna K Simonsen
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Koffler Scientific Reserve, University of Toronto, King, ON, L7B 1K5, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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12
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Wood CW, Pilkington BL, Vaidya P, Biel C, Stinchcombe JR. Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism. Evol Lett 2018; 2:233-245. [PMID: 30283679 PMCID: PMC6121810 DOI: 10.1002/evl3.51] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/07/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness‐related traits. Here, we tested whether susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen‐fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root‐knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode‐infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.
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Affiliation(s)
- Corlett W Wood
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario M5S3B2 Canada
| | - Bonnie L Pilkington
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario M5S3B2 Canada
| | - Priya Vaidya
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario M5S3B2 Canada
| | - Caroline Biel
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario M5S3B2 Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario M5S3B2 Canada.,Koffler Scientific Reserve University of Toronto Toronto Ontario M5S3B2 Canada
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13
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Pain RE, Shaw RG, Sheth SN. Detrimental effects of rhizobial inoculum early in the life of partridge pea, Chamaecrista fasciculata. AMERICAN JOURNAL OF BOTANY 2018; 105:796-802. [PMID: 29768658 DOI: 10.1002/ajb2.1077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Mutualistic relationships with microbes may aid plants in overcoming environmental stressors and increase the range of abiotic environments where plants can persist. Rhizobia, nitrogen-fixing bacteria associated with legumes, often confer fitness benefits to their host plants by increasing access to nitrogen in nitrogen-limited soils, but effects of rhizobia on host fitness under other stresses, such as drought, remain unclear. METHODS In this greenhouse study, we varied the application of rhizobia (Bradyrhizobium sp.) inoculum and drought to examine whether the fitness benefits of rhizobia to their host, partridge pea (Chamaecrista fasciculata), would differ between drought and well-watered conditions. Plants were harvested 9 weeks after seeds were sown. KEY RESULTS Young C. fasciculata plants that had been inoculated had lower biomass, leaf relative growth rate, and stem relative growth rate compared to young uninoculated plants in both drought and well-watered environments. CONCLUSIONS Under the conditions of this study, the rhizobial interaction imposed a net cost to their hosts early in development. Potential reasons for this cost include allocating more carbon to nodule and root development than to aboveground growth and a geographic mismatch between the source populations of host plants and rhizobia. If developing plants incur such costs from rhizobia in nature, they may suffer an early disadvantage relative to other plants, whether conspecifics lacking rhizobia or heterospecifics.
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Affiliation(s)
- Rachel E Pain
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Ruth G Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Seema N Sheth
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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14
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Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:81-89. [PMID: 29694936 DOI: 10.1016/j.pbi.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/24/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
Selective sweeps may be caused by environmental conditions that select for a gene function or trait at one locus, causing reduced variation at neighboring sites due to linkage, with specific non-selected variants being swept along with the selected variant. For many species, genomic and environmental data are available to test hypotheses that environmental conditions are correlated with selected regions. Most genomic studies relating selection to environment use model organisms or crop species; typically, these studies have genomic data from large numbers of individuals and extensive environmental data. Here, we review studies associating selective sweeps with environment and consider the impediments to successful application of these methods to non-model species. We present an initial investigation into linking genomic regions of selection to environmental conditions in the narrowly distributed, non-model plant Amborella trichopoda (Amborellaceae), the sister species to all other living flowering plants and one of over 2500 plant species endemic to New Caledonia.
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Affiliation(s)
- Richard Gj Hodel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Luke M Chandler
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
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15
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Storfer A, Patton A, Fraik AK. Navigating the Interface Between Landscape Genetics and Landscape Genomics. Front Genet 2018; 9:68. [PMID: 29593776 PMCID: PMC5859105 DOI: 10.3389/fgene.2018.00068] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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16
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Harrison TL, Wood CW, Borges IL, Stinchcombe JR. No evidence for adaptation to local rhizobial mutualists in the legume Medicago lupulina. Ecol Evol 2017; 7:4367-4376. [PMID: 28649348 PMCID: PMC5478075 DOI: 10.1002/ece3.3012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/15/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022] Open
Abstract
Local adaptation is a common but not ubiquitous feature of species interactions, and understanding the circumstances under which it evolves illuminates the factors that influence adaptive population divergence. Antagonistic species interactions dominate the local adaptation literature relative to mutualistic ones, preventing an overall assessment of adaptation within interspecific interactions. Here, we tested whether the legume Medicago lupulina is adapted to the locally abundant species of mutualistic nitrogen-fixing rhizobial bacteria that vary in frequency across its eastern North American range. We reciprocally inoculated northern and southern M. lupulina genotypes with the northern (Ensifer medicae) or southern bacterium (E. meliloti) in a greenhouse experiment. Despite producing different numbers of root nodules (the structures in which the plants house the bacteria), neither northern nor southern plants produced more seeds, flowered earlier, or were more likely to flower when inoculated with their local rhizobia. We then used a pre-existing dataset to perform a genome scan for loci that showed elevated differentiation between field-collected plants that hosted different bacteria. None of the loci we identified belonged to the well-characterized suite of legume-rhizobia symbiosis genes, suggesting that the rhizobia do not drive genetic divergence between M. lupulina populations. Our results demonstrate that symbiont local adaptation has not evolved in this mutualism despite large-scale geographic variation in the identity of the interacting species.
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Affiliation(s)
- Tia L. Harrison
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Corlett W. Wood
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Isabela L. Borges
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Centre for Genome Evolution and FunctionUniversity of TorontoTorontoONCanada
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