1
|
Westgeest AJ, Vasseur F, Enquist BJ, Milla R, Gómez-Fernández A, Pot D, Vile D, Violle C. An allometry perspective on crops. THE NEW PHYTOLOGIST 2024. [PMID: 39288438 DOI: 10.1111/nph.20129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024]
Abstract
Understanding trait-trait coordination is essential for successful plant breeding and crop modeling. Notably, plant size drives variation in morphological, physiological, and performance-related traits, as described by allometric laws in ecology. Yet, as allometric relationships have been limitedly studied in crops, how they influence and possibly limit crop performance remains unknown. Here, we review how an allometry perspective on crops gains insights into the phenotypic evolution during crop domestication, the breeding of varieties adapted to novel conditions, and the prediction of crop yields. As allometry is an active field of research, modeling and manipulating crop allometric relationships can help to develop more resilient and productive agricultural systems to face future challenges.
Collapse
Affiliation(s)
- Adrianus J Westgeest
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34090, France
- Département Biologie et Ecologie, Institut Agro, Montpellier, 34060, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34090, France
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85719, USA
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Rubén Milla
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, C/Tulipán s/n, Móstoles, 28933, Spain
| | - Alicia Gómez-Fernández
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34090, France
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, C/Tulipán s/n, Móstoles, 28933, Spain
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, 34980, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, 34980, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, 34060, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34090, France
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Golan G, Weiner J, Zhao Y, Schnurbusch T. Agroecological genetics of biomass allocation in wheat uncovers genotype interactions with canopy shade and plant size. THE NEW PHYTOLOGIST 2024; 242:107-120. [PMID: 38326944 DOI: 10.1111/nph.19576] [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: 09/09/2023] [Accepted: 01/21/2024] [Indexed: 02/09/2024]
Abstract
How plants distribute biomass among organs influences resource acquisition, reproduction and plant-plant interactions, and is essential in understanding plant ecology, evolution, and yield production in agriculture. However, the genetic mechanisms regulating allocation responses to the environment are largely unknown. We studied recombinant lines of wheat (Triticum spp.) grown as single plants under sunlight and simulated canopy shade to investigate genotype-by-environment interactions in biomass allocation to the leaves, stems, spikes, and grains. Size-corrected mass fractions and allometric slopes were employed to dissect allocation responses to light limitation and plant size. Size adjustments revealed light-responsive alleles associated with adaptation to the crop environment. Combined with an allometric approach, we demonstrated that polymorphism in the DELLA protein is associated with the response to shade and size. While a gibberellin-sensitive allelic effect on stem allocation was amplified when plants were shaded, size-dependent effects of this allele drive allocation to reproduction, suggesting that the ontogenetic trajectory of the plant affects the consequences of shade responses for allocation. Our approach provides a basis for exploring the genetic determinants underlying investment strategies in the face of different resource constraints and will be useful in predicting social behaviours of individuals in a crop community.
Collapse
Affiliation(s)
- Guy Golan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
| | - Jacob Weiner
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871, Frederiksberg, Denmark
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120, Halle, Germany
| |
Collapse
|
4
|
Zhou H, McPeek MS. Overcoming the "feast or famine" effect: improved interaction testing in genome-wide association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580168. [PMID: 38405994 PMCID: PMC10888770 DOI: 10.1101/2024.02.13.580168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In genetic association analysis of complex traits, detection of interaction (either GxG or GxE) can help to elucidate the genetic architecture and biological mechanisms underlying the trait. Detection of interaction in a genome-wide association study (GWAS) can be methodologically challenging for various reasons, including a high burden of multiple comparisons when testing for epistasis between all possible pairs of a set of genomewide variants, as well as heteroscedasticity effects occurring in the presence of GxG or GxE interaction. In this paper, we address the problem of an even more striking phenomenon that we call the "feast or famine" effect that occurs when testing interaction in a genomewide context. As we verify, even in a simplified setting in which there is no interaction at all (and so no heteroscedasticity), in a GWAS to detect GxG or GxE interaction with a fixed genetic variant or environmental factor, the distribution of the genome-wide p-values under the null hypothesis is not the i.i.d. uniform one that is commonly assumed. Using standard methods, even if all SNPs are independent, some GWASs will have systematically underinflated p-values ("feast"), and others will have systematically overinflated p-values ("famine"), which can lead to false detection of interaction, reduced power, inconsistent results across studies, and failure to replicate true signal. This startling phenomenon is specific to detection of interaction in a GWAS, and it may partly explain why such detection has so far proved challenging and difficult to replicate. We show theoretically that the key cause of this phenomenon is which variables are conditioned on in the analysis, and this suggests an approach to correct the problem by changing the way the conditioning is done. Using this insight, we have developed the TINGA method to adjust the interaction test statistics to make their p-values closer to uniform under the null hypothesis. In simulations we show that TINGA both controls type 1 error and improves power. TINGA allows for covariates and population structure through use of a linear mixed model and accounts for heteroscedasticity. We apply TINGA to detection of epistasis in a study of flowering time in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Huanlin Zhou
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, U.S.A
| |
Collapse
|
5
|
Chien PS, Chen PH, Lee CR, Chiou TJ. Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5653-5666. [PMID: 37419660 DOI: 10.1093/jxb/erad262] [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: 12/07/2022] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
Genome-wide association study (GWAS) has improved our understanding of complex traits, but challenges exist in distinguishing causation versus association caused by linkage disequilibrium. Instead, transcriptome-wide association studies (TWAS) detect direct associations between expression levels and phenotypic variations, providing an opportunity to better prioritize candidate genes. To assess the feasibility of TWAS, we investigated the association between transcriptomes, genomes, and various traits in Arabidopsis, including flowering time. The associated genes formerly known to regulate growth allometry or metabolite production were first identified by TWAS. Next, for flowering time, six TWAS-newly identified genes were functionally validated. Analysis of the expression quantitative trait locus (eQTL) further revealed a trans-regulatory hotspot affecting the expression of several TWAS-identified genes. The hotspot covers the FRIGIDA (FRI) gene body, which possesses multiple haplotypes differentially affecting the expression of downstream genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). We also revealed multiple independent paths towards the loss of function of FRI in natural accessions. Altogether, this study demonstrates the potential of combining TWAS with eQTL analysis to identify important regulatory modules of FRI-FLC-SOC1 for quantitative traits in natural populations.
Collapse
Affiliation(s)
- Pei-Shan Chien
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Pin-Hua Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
6
|
Lamont BB, Williams MR, He T. Relative growth rate (RGR) and other confounded variables: mathematical problems and biological solutions. ANNALS OF BOTANY 2023; 131:555-568. [PMID: 36794962 PMCID: PMC10147329 DOI: 10.1093/aob/mcad031] [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: 11/05/2022] [Accepted: 02/14/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Relative growth rate (RGR) has a long history of use in biology. In its logged form, RGR = ln[(M + ΔM)/M], where M is size of the organism at the commencement of the study, and ΔM is new growth over time interval Δt. It illustrates the general problem of comparing non-independent (confounded) variables, e.g. (X + Y) vs. X. Thus, RGR depends on what starting M(X) is used even within the same growth phase. Equally, RGR lacks independence from its derived components, net assimilation rate (NAR) and leaf mass ratio (LMR), as RGR = NAR × LMR, so that they cannot legitimately be compared by standard regression or correlation analysis. FINDINGS The mathematical properties of RGR exemplify the general problem of 'spurious' correlations that compare expressions derived from various combinations of the same component terms X and Y. This is particularly acute when X >> Y, the variance of X or Y is large, or there is little range overlap of X and Y values among datasets being compared. Relationships (direction, curvilinearity) between such confounded variables are essentially predetermined and so should not be reported as if they are a finding of the study. Standardizing by M rather than time does not solve the problem. We propose the inherent growth rate (IGR), lnΔM/lnM, as a simple, robust alternative to RGR that is independent of M within the same growth phase. CONCLUSIONS Although the preferred alternative is to avoid the practice altogether, we discuss cases where comparing expressions with components in common may still have utility. These may provide insights if (1) the regression slope between pairs yields a new variable of biological interest, (2) the statistical significance of the relationship remains supported using suitable methods, such as our specially devised randomization test, or (3) multiple datasets are compared and found to be statistically different. Distinguishing true biological relationships from spurious ones, which arise from comparing non-independent expressions, is essential when dealing with derived variables associated with plant growth analyses.
Collapse
Affiliation(s)
- Byron B Lamont
- Ecology Section, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Matthew R Williams
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation & Attractions, Kensington, WA 6151, Australia
| | - Tianhua He
- Ecology Section, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| |
Collapse
|
7
|
Cheng L. Superlinear urban scaling by functional organization: A metabolic interpretation of sectoral water consumption. Phys Rev E 2023; 107:034301. [PMID: 37072995 DOI: 10.1103/physreve.107.034301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/11/2023] [Indexed: 04/20/2023]
Abstract
Prevailing view asserts that the disproportionately greater productivities of larger cities, or superlinear urban scaling, are the result of human interactions channeled by urban networks. But this view was established by considering the spatial organization of urban infrastructure and social networks-the urban "arteries" effects-but neglecting the functional organization of urban production and consumption entities-the urban "organs" effects. Here, adopting a metabolic view and using water consumption as a proxy for metabolism, we empirically quantify the scaling of entity number, size, and metabolic rate for the functionally specific urban residential, commercial, public or institutional, and industrial sectors. Sectoral urban metabolic scaling is highlighted by a disproportionate coordination between residential and enterprise metabolic rates, attributable to the functional mechanisms of mutualism, specialization, and entity size effect. The resultant whole-city metabolic scaling exhibits a constant superlinear exponent for water-abundant regions in numerical agreement with superlinear urban productivity, with varying exponent deviations for water-deficient regions explainable as adaptations to climate-driven resource constraints. These results present a functional organizational, non-social-network explanation of superlinear urban scaling.
Collapse
Affiliation(s)
- Likwan Cheng
- Physical Science Department, City Colleges of Chicago-Harold Washington College, Chicago, Illinois 60601, USA
| |
Collapse
|
8
|
Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
Collapse
Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
| | | |
Collapse
|
9
|
Hjertaas AC, Preston JC, Kainulainen K, Humphreys AM, Fjellheim S. Convergent evolution of the annual life history syndrome from perennial ancestors. FRONTIERS IN PLANT SCIENCE 2023; 13:1048656. [PMID: 36684797 PMCID: PMC9846227 DOI: 10.3389/fpls.2022.1048656] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.
Collapse
Affiliation(s)
- Ane C. Hjertaas
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, United States
| | - Kent Kainulainen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Aelys M. Humphreys
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
10
|
Yu G, Derkacheva M, Rufian JS, Brillada C, Kowarschik K, Jiang S, Derbyshire P, Ma M, DeFalco TA, Morcillo RJL, Stransfeld L, Wei Y, Zhou J, Menke FLH, Trujillo M, Zipfel C, Macho AP. The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector. EMBO J 2022; 41:e107257. [PMID: 36314733 PMCID: PMC9713774 DOI: 10.15252/embj.2020107257] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 12/03/2022] Open
Abstract
Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogen Ralstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.
Collapse
Affiliation(s)
- Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Maria Derkacheva
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
- Present address:
The Earlham InstituteNorwich Research ParkNorwichUK
| | - Jose S Rufian
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Carla Brillada
- Faculty of Biology, Institute of Biology IIAlbert‐Ludwigs‐University FreiburgFreiburgGermany
| | | | - Shushu Jiang
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
- Present address:
Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Paul Derbyshire
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Miaomiao Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Thomas A DeFalco
- Institute of Plant and Microbial Biology, Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
| | - Rafael J L Morcillo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Lena Stransfeld
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
- Institute of Plant and Microbial Biology, Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
| | - Yali Wei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian‐Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Frank L H Menke
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Marco Trujillo
- Faculty of Biology, Institute of Biology IIAlbert‐Ludwigs‐University FreiburgFreiburgGermany
- Leibniz Institute for Plant BiochemistryHalle (Saale)Germany
| | - Cyril Zipfel
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
- Institute of Plant and Microbial Biology, Zurich‐Basel Plant Science CenterUniversity of ZurichZurichSwitzerland
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| |
Collapse
|
11
|
Fletcher LR, Scoffoni C, Farrell C, Buckley TN, Pellegrini M, Sack L. Testing the association of relative growth rate and adaptation to climate across natural ecotypes of Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:413-432. [PMID: 35811421 DOI: 10.1111/nph.18369] [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: 01/20/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Ecophysiologists have reported a range of relationships, including intrinsic trade-offs across and within species between plant relative growth rate in high resource conditions (RGR) vs adaptation to tolerate cold or arid climates, arising from trait-based mechanisms. Few studies have considered ecotypes within a species, in which the lack of a trade-off would contribute to a wide species range and resilience to climate change. For 15 ecotypes of Arabidopsis thaliana in a common garden we tested for associations between RGR vs adaptation to cold or dry native climates and assessed hypotheses for its mediation by 15 functional traits. Ecotypes native to warmer, drier climates had higher leaf density, leaf mass per area, root mass fraction, nitrogen per leaf area and carbon isotope ratio, and lower osmotic potential at full turgor. Relative growth rate was statistically independent of the climate of the ecotype native range and of individual functional traits. The decoupling of RGR and cold or drought adaptation in Arabidopsis is consistent with multiple stress resistance and avoidance mechanisms for ecotypic climate adaptation and would contribute to the species' wide geographic range and resilience as the climate changes.
Collapse
Affiliation(s)
- Leila R Fletcher
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
- School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Christine Scoffoni
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Thomas N Buckley
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA, 95616, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Bajpai PK, Harel A, Shafir S, Barazani O. Whole genome sequencing reveals footprints of adaptive genetic variation in populations of Eruca sativa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.938981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Populations of Eruca sativa (Brassicaceae) derived from arid and Mediterranean habitats exhibit ecotypic differentiation. Here, pooled DNA sequencing was used to assess adaptive genome differentiation in the two ecotypes. Differentiated SNP loci were scanned with the empirical FST outlier method and by correlating allele frequencies with environmental parameters. Genetic diversity values were relatively higher in the pooled arid genome, whereas the pooled Mediterranean genome exhibited stronger directional selection, indicating the impact of climatic conditions on genetic diversity. GO enrichment analysis categorized the annotated differentiated loci according to biological processes, revealing a large set of candidate genes related to abiotic and biotic stress responses. Allelic variation was detected in regulatory elements and coding regions (synonymous and non-synonymous mutations) of genes belonging to different transcription factors and phytohormone signaling, suggesting adaptation to both abiotic and biotic conditions. Furthermore, SNP mutations were also found in genic regions belonging to the synthesis of secondary metabolites, including aliphatic glucosinolates and their hydrolyzed bioactive compounds, among others. The results of this eco-genomic study demonstrate the role of divergent abiotic and biotic selection factors in evolutionary processes leading to adaptive ecotypic differentiation.
Collapse
|
14
|
Khan N, Ullah R, Alamri SS, Alwasel YA, AL-Hashimi A, Abdel-Maksoud MA, Okla MK, AbdElgawad H. Environment-Driven Changes in the Functional Traits of Milk Thistle [ Silybum marianum (L). Gaertn.] Along an Altitudinal Gradient in the Semi-Arid Environment: Perspective on Future Plant Invasion. FRONTIERS IN PLANT SCIENCE 2022; 13:897678. [PMID: 35832234 PMCID: PMC9271949 DOI: 10.3389/fpls.2022.897678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The elevation is an important gradient across which the environmental variables and plant traits vary and is considered as a barrier to the recent global problem of plant invasion. However, certain invasive plants show plasticity traits to adapt and cope with the changes across the elevation. Silybum marianum (S. marianum) is one such invasive species widely spread in Khyber Pakhtunkhwa, Pakistan. Therefore, this study investigates the traits plasticity and invasive behaviors of this plant species across the elevation gradient. Plant functional traits (PFTs) and environmental variables were recorded in forty different low, middle, and high elevation sites. The plant shows a decrease in plant functional traits, i.e., above-ground plant height/plant, leaf length/leaf, leaf width/leaf, leaf dry weight/plant, vegetative dry weight/plant, and number of capitula/plant having the significance of p < 0.05. In contrast, the dry reproductive weight does not change significantly with elevation, while the root length increases across the elevation. The soil and environmental variables such as organic matter, lime percentage, and latitude significantly affected the PFTs. The importance value index of the species was also related to elevation and diversity indices, i.e., species richness, Shannon-Wiener diversity index, and evenness index, indicating that the invasion has strong effects on diversity. This study concludes that S. marianum has traits plasticity across the elevation and affects community diversity. Further investigation is required to understand the invasion and diversity parameters in a better way.
Collapse
Affiliation(s)
- Nasrullah Khan
- Department of Botany, University of Malakand, Chakdara, Pakistan
| | - Rafi Ullah
- Department of Botany, University of Malakand, Chakdara, Pakistan
| | - Saud S. Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yasmeen A. Alwasel
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman AL-Hashimi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafa A. Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K. Okla
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hamada AbdElgawad
- Laboratory for Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
15
|
Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:93-121. [PMID: 35226816 DOI: 10.1146/annurev-arplant-102720-012310] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.
Collapse
Affiliation(s)
- Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | | | - Bushra Saeed
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany; ,
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA;
| | - Marco Trujillo
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; ,
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Thakur D, Münzbergová Z. Rhizome trait scaling relationships are modulated by growth conditions and are linked to plant fitness. ANNALS OF BOTANY 2022; 129:529-540. [PMID: 35180294 PMCID: PMC9007095 DOI: 10.1093/aob/mcac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Rhizomes are important organs allowing many clonal plants to persist and reproduce under stressful climates with longer rhizomes, indicating enhanced ability of the plants to spread vegetatively. We do not, however, know either how rhizome construction costs change with increasing length or how they vary with environmental conditions. METHODS We analysed the rhizome length vs. mass scaling relationship, the plasticity in the scaling relationships, their genetic basis and how scaling relationships are linked to plant fitness. We used data from 275 genotypes of a clonal grass Festuca rubra originating from 11 localities and cultivated under four contrasting climates. Data were analysed using standard major axis regression, mixed-effect regression models and a structural equation model. KEY RESULTS Rhizome construction costs increased (i.e. lower specific rhizome length) with increasing length. The trait scaling relationships were modulated by cultivation climate, and its effects also interacted with the climate of origin of the experimental plants. With increasing length, increasing moisture led to a greater increase in rhizome construction costs. Plants with lower rhizome construction costs showed significantly higher fitness. CONCLUSIONS This study suggests that rhizome scaling relationships are plastic, but also show genetic differentiation and are linked to plant fitness. Therefore, to persist under variable environments, modulation in scaling relationships could be an important plant strategy.
Collapse
Affiliation(s)
- Dinesh Thakur
- Institute of Botany, Czech Academy of Sciences, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
18
|
Wang Y, Wu Y, Zhong H, Chen S, Wong KB, Xia Y. Arabidopsis PUB2 and PUB4 connect signaling components of pattern-triggered immunity. THE NEW PHYTOLOGIST 2022; 233:2249-2265. [PMID: 34918346 DOI: 10.1111/nph.17922] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Plants use pattern recognition receptors (PRRs) to detect pathogen-associated molecular patterns (PAMPs) and activate pattern-triggered immunity (PTI). Precise regulation of information from PRRs to downstream signaling components is vital to mounting an appropriate immune response and requires dynamic interactions of these PTI components. We used transcriptome profiling, phenotypic analysis, molecular genetics, and protein-protein interaction analysis to understand the roles of the Arabidopsis plant U-box (PUB) proteins PUB2 and PUB4 in disease resistance and PTI signaling. Loss of function of both PUB2 and PUB4 diminishes the PAMP-triggered oxidative bursts and dampens mitogen-activated protein kinase signaling, resulting in a severe compromise in resistance to not only pathogenic but also nonpathogenic strains of Pseudomonas syringae. Within PUB4, the E3 ligase activity is dispensable, but the armadillo repeat region is essential and sufficient for its function in immunity. PUB2 and PUB4 interact with PTI signaling components, including FLS2, BIK1, PBL27, and RbohD, and enhance FLS2-BIK1 and BIK1-RbohD interactions. Our study reveals that PUB2 and PUB4 are critical components of plant immunity and connect PTI components to positively regulate defense responses.
Collapse
Affiliation(s)
- Yiping Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shen Zhen, 518057, China
| | - Yingying Wu
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Huan Zhong
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Shuai Chen
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Kam-Bo Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, 999077, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
- State Key Laboratory of Biological and Environmental Analysis, Hong Kong Baptist University, Hong Kong, 999077, China
| |
Collapse
|
19
|
Estarague A, Vasseur F, Sartori K, Bastias CC, Cornet D, Rouan L, Beurier G, Exposito-Alonso M, Herbette S, Bresson J, Vile D, Violle C. Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana? ANNALS OF BOTANY 2022; 129:343-356. [PMID: 34918027 PMCID: PMC8835660 DOI: 10.1093/aob/mcab149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species' ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies from the CSR scheme and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center- margins gradient within the native range of Arabidopsis thaliana. METHODS We experimentally examined the phenotypic outcomes of plant adaptation at the center and margins of its geographic range using 30 accessions from southern, central and northern Europe. We characterized the variation of traits related to stress tolerance, resource use, colonization ability, CSR strategy scores, survival and fecundity in response to high temperature (34 °C) or frost (- 6 °C), combined with a water deficit treatment. KEY RESULTS We found evidence for both a latitudinal and a center-margins differentiation for the traits under scrutiny. Age at maturity, leaf dry matter content, specific leaf area and leaf nitrogen content varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Leaf area, C-scores, R-scores and fruit number followed a center-margins differentiation. Central accessions displayed a higher phenotypic plasticity than northern and southern accessions for most studied traits. CONCLUSIONS Traits related to an acquisitive/conservative resource-use trade-off followed a latitudinal gradient. Traits associated with a competition/colonization trade-off differentiated along the historic colonization of the distribution range and then followed a center-margins differentiation. Our findings pinpoint the need to consider the joint effect of evolutionary history and environmental factors when examining phenotypic variation across the distribution range of a species.
Collapse
Affiliation(s)
- Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRAE, Montpellier SupAgro, UMR759, F-34060, Montpellier, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
| | - Kevin Sartori
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Denis Cornet
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Gregory Beurier
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Justine Bresson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
| | - Denis Vile
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRAE, Montpellier SupAgro, UMR759, F-34060, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
| |
Collapse
|
20
|
Ullah R, Khan N, Ali K. Which factor explains the life-history of Xanthium strumarium L., an aggressive alien invasive plant species, along its altitudinal gradient? PLANT DIRECT 2022; 6:e375. [PMID: 35028495 PMCID: PMC8743363 DOI: 10.1002/pld3.375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 05/09/2023]
Abstract
Invasive biology acknowledges the concept of better performance by invasive plants in the introduced range. Xanthium strumarium L. is one of the successful invasive species in Khyber Pakhtunkhwa, Pakistan. The phenological pattern, vegetative and reproductive traits plasticity analysis of the species was explored to explain the invasive success across the altitudinal gradient in the current invaded habitats. Phenological patterns and timing (seedling, vegetative growth, flowering and fruiting, drying, and seed bank) were observed during a full year for two seasons. We also examine plant functional traits at altitudes of 500, 1000, and 1500 m a.s.l. to assess traits and biomass variations. The X. strumarium exhibits late vegetative and reproductive phenology at higher altitudes, enabling them to occupy an empty niche and benefit from decreased competition for resource acquisition. The lower altitude plants show a higher growth rate (stem size increase, number of leaves, and leaf area) due to the higher nutrient availability. Higher altitude plants have the highest reproductive biomass and biomass ratio revealing plant abilities to be reproductively adapted in the higher altitudes. Among climatic variables, mean yearly temperature, mean annual yearly humidity, and mean day length in hours, while in soil variables, organic matter and nitrogen percentage significantly affect the phenological and morphological stages. Therefore, we conclude that X. strumarium can invade higher altitudes with a shift in its phenological and morphological changes making the invasion process successful.
Collapse
Affiliation(s)
- Rafi Ullah
- Department of BotanyUniversity of MalakandChakdaraPakistan
| | - Nasrullah Khan
- Department of BotanyUniversity of MalakandChakdaraPakistan
| | - Kishwar Ali
- School of General EducationCollege of the North Atlantic – QatarDohaQatar
| |
Collapse
|
21
|
Bergès SE, Vile D, Yvon M, Masclef D, Dauzat M, van Munster M. Water deficit changes the relationships between epidemiological traits of Cauliflower mosaic virus across diverse Arabidopsis thaliana accessions. Sci Rep 2021; 11:24103. [PMID: 34916537 PMCID: PMC8677750 DOI: 10.1038/s41598-021-03462-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022] Open
Abstract
Changes in plant abiotic environments may alter plant virus epidemiological traits, but how such changes actually affect their quantitative relationships is poorly understood. Here, we investigated the effects of water deficit on Cauliflower mosaic virus (CaMV) traits (virulence, accumulation, and vectored-transmission rate) in 24 natural Arabidopsis thaliana accessions grown under strictly controlled environmental conditions. CaMV virulence increased significantly in response to water deficit during vegetative growth in all A. thaliana accessions, while viral transmission by aphids and within-host accumulation were significantly altered in only a few. Under well-watered conditions, CaMV accumulation was correlated positively with CaMV transmission by aphids, while under water deficit, this relationship was reversed. Hence, under water deficit, high CaMV accumulation did not predispose to increased horizontal transmission. No other significant relationship between viral traits could be detected. Across accessions, significant relationships between climate at collection sites and viral traits were detected but require further investigation. Interactions between epidemiological traits and their alteration under abiotic stresses must be accounted for when modelling plant virus epidemiology under scenarios of climate change.
Collapse
Affiliation(s)
- Sandy E Bergès
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France.
| | - Michel Yvon
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Diane Masclef
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Myriam Dauzat
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | |
Collapse
|
22
|
Levionnois S, Salmon C, Alméras T, Clair B, Ziegler C, Coste S, Stahl C, González-Melo A, Heinz C, Heuret P. Anatomies, vascular architectures, and mechanics underlying the leaf size-stem size spectrum in 42 Neotropical tree species. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7957-7969. [PMID: 34390333 DOI: 10.1093/jxb/erab379] [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: 02/05/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The leaf size-stem size spectrum is one of the main dimensions of plant ecological strategies. Yet the anatomical, mechanical, and hydraulic implications of small versus large shoots are still poorly understood. We investigated 42 tropical rainforest tree species in French Guiana, with a wide range of leaf areas at the shoot level. We quantified the scaling of hydraulic and mechanical constraints with shoot size, estimated as the water potential difference (ΔΨ) and the bending angle (ΔΦ), respectively. We investigated how anatomical tissue area, flexural stiffness and xylem vascular architecture affect such scaling by deviating (or not) from theoretical isometry with shoot size variation. Vessel diameter and conductive path length were found to be allometrically related to shoot size, thereby explaining the independence between ΔΨ and shoot size. Leaf mass per area, stem length, and the modulus of elasticity were allometrically related to shoot size, explaining the independence between ΔΦ and shoot size. Our study also shows that the maintenance of both water supply and mechanical stability across the shoot size range are not in conflict.
Collapse
Affiliation(s)
- Sébastien Levionnois
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310 Kourou, France
- UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Université de Montpellier, 34000 Montpellier, France
| | - Camille Salmon
- UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Université de Montpellier, 34000 Montpellier, France
| | - Tancrède Alméras
- LMGC, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Bruno Clair
- LMGC, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Camille Ziegler
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310 Kourou, France
- UMR SILVA, INRAE, Université de Lorraine, 54000 Nancy, France
| | - Sabrina Coste
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310 Kourou, France
| | - Clément Stahl
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310 Kourou, France
| | | | - Christine Heinz
- UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Université de Montpellier, 34000 Montpellier, France
| | - Patrick Heuret
- UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Université de Montpellier, 34000 Montpellier, France
| |
Collapse
|
23
|
Gaudio N, Violle C, Gendre X, Fort F, Mahmoud R, Pelzer E, Médiène S, Hauggaard‐Nielsen H, Bedoussac L, Bonnet C, Corre‐Hellou G, Couëdel A, Hinsinger P, Steen Jensen E, Journet E, Justes E, Kammoun B, Litrico I, Moutier N, Naudin C, Casadebaig P. Interspecific interactions regulate plant reproductive allometry in cereal–legume intercropping systems. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Noémie Gaudio
- AGIRUniversité de ToulouseINRAE Castanet‐Tolosan France
| | - Cyrille Violle
- UMR 5175 CEFE Univ. MontpellierCNRSEPHEIRD Montpellier France
| | | | - Florian Fort
- UMR 5175 CEFE Univ. MontpellierCNRSEPHEInstitut AgroIRD Montpellier France
| | - Rémi Mahmoud
- AGIRUniversité de ToulouseINRAE Castanet‐Tolosan France
| | - Elise Pelzer
- Université Paris‐SaclayAgroParisTechINRAEUMR Agronomie Thiverval‐Grignon France
| | - Safia Médiène
- Université Paris‐SaclayAgroParisTechINRAEUMR Agronomie Thiverval‐Grignon France
| | | | | | | | | | | | - Philippe Hinsinger
- Eco&SolsUniversité de MontpellierINRAE, CIRADInstitut AgroIRD Montpellier France
| | - Erik Steen Jensen
- Cropping Systems EcologyDepartment of Biosystems and Technology Alnarp Sweden
| | - Etienne‐Pascal Journet
- AGIRUniversité de ToulouseINRAE Castanet‐Tolosan France
- LIPMEUniversité de ToulouseCNRS Castanet‐Tolosan France
| | - Eric Justes
- AGIRUniversité de ToulouseINRAE Castanet‐Tolosan France
- CIRADPersyst Department Montpellier France
| | | | | | | | - Christophe Naudin
- USC ESA‐INRAE LEVAEcole Supérieure d’Agricultures Angers Cedex France
| | | |
Collapse
|
24
|
Yan W, Wang B, Chan E, Mitchell-Olds T. Genetic architecture and adaptation of flowering time among environments. THE NEW PHYTOLOGIST 2021; 230:1214-1227. [PMID: 33484593 PMCID: PMC8193995 DOI: 10.1111/nph.17229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/07/2021] [Indexed: 05/17/2023]
Abstract
The genetic basis of flowering time changes across environments, and pleiotropy may limit adaptive evolution of populations in response to local conditions. However, little information is known about how genetic architecture changes among environments. We used genome-wide association studies (GWAS) in Boechera stricta (Graham) Al-Shehbaz, a relative of Arabidopsis, to examine flowering variation among environments and associations with climate conditions in home environments. Also, we used molecular population genetics to search for evidence of historical natural selection. GWAS found 47 significant quantitative trait loci (QTLs) that influence flowering time in one or more environments, control plastic changes in phenology between experiments, or show associations with climate in sites of origin. Genetic architecture of flowering varied substantially among environments. We found that some pairs of QTLs showed similar patterns of pleiotropy across environments. A large-effect QTL showed molecular signatures of adaptive evolution and is associated with climate in home environments. The derived allele at this locus causes later flowering and predominates in sites with greater water availability. This work shows that GWAS of climate associations and ecologically important traits across diverse environments can be combined with molecular signatures of natural selection to elucidate ecological genetics of adaptive evolution.
Collapse
Affiliation(s)
- Wenjie Yan
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Emily Chan
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | | |
Collapse
|
25
|
Mainali S, Colorado FA, Garzon MH. Foretelling the Phenotype of a Genomic Sequence. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:777-783. [PMID: 32287003 DOI: 10.1109/tcbb.2020.2985349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Estimating phenotypic features (physical and biochemical traits) in a biological organism from their genomic sequence alone and/or environmental conditions has major applications in anthropological paleontology and criminal forensics, for example. To what extent do genomic sequences generally and causally determine phenotypic features of organisms, environmental conditions aside? We present results of two studies, one in blackfly (Insecta:Diptera:Simuliidae) larvae in two species (Simulium ignescens and S. tunja) with four phenotypic features, including the area and spot pattern of the cephalic apotome (in the form of a latin cross on the dorsal side of the head), the postgenal cleft (area under the head on the ventral side) and general body color in larva specimens; the second in strains of Arabidopsis thaliana. They establish that a substantial component of these phenotypic features (over 75 percent) are at least logically inferable, if not causally determined, by genomic fragments alone, despite the fact that these phenotypic features are not 100 percent determined entirely by genetic traits. These results suggest that it is possible to infer the genetic contribution in the determination of specific phenotypic features of a biological organism, without recourse to the causal chain of metabolomics and proteomic events leading to them from genomic sequences.
Collapse
|
26
|
Wieters B, Steige KA, He F, Koch EM, Ramos-Onsins SE, Gu H, Guo YL, Sunyaev S, de Meaux J. Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLoS Genet 2021; 17:e1008748. [PMID: 33493157 PMCID: PMC7861555 DOI: 10.1371/journal.pgen.1008748] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 02/04/2021] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution. The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its genetic variation in natural populations. Here, we investigate genetic and environmental factors shaping variation in the growth rate of Arabidopsis thaliana and ask whether genetic variation in plant growth contributes to adaptation to local environmental conditions. We grew plants under two light regimes that mimic latitudinal differences in the intensity of natural light radiation, and measured plant diameter as it grew over time. When the light supply was decreased, plant diameter grew more slowly but reached a markedly larger final size, confirming that plants can adjust their growth to prevailing light conditions. Yet, we also detected significant levels of genetic variation both in growth rate and in how the growth dynamics is adjusted to the light conditions. We show that this variation is encoded by many loci of small effect that are hard to locate in the genome but overall significantly enriched among genes associated with growth and stress reactions. We further observe that Spanish genotypes tended to reach, on average, a significantly larger rosette size than Northern European genotypes. Tests of adaptive divergence indicate that these differences may reflect adaptation to local environmental conditions.
Collapse
Affiliation(s)
| | - Kim A. Steige
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Fei He
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Evan M. Koch
- Genetics Division, Brigham & Women's Hospital and Harvard Medical School, Boston MA, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston MA, United States of America
| | | | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shamil Sunyaev
- Genetics Division, Brigham & Women's Hospital and Harvard Medical School, Boston MA, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston MA, United States of America
| | - Juliette de Meaux
- Institute of Botany, University of Cologne, Cologne, Germany
- * E-mail:
| |
Collapse
|
27
|
Xiao Y, Liu X, Zhang L, Song Z, Zhou S. The allometry of plant height explains species loss under nitrogen addition. Ecol Lett 2021; 24:553-562. [PMID: 33423373 DOI: 10.1111/ele.13673] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 12/22/2022]
Abstract
Light asymmetry, with a higher light acquisition per unit biomass for larger plants, has been proposed as a major mechanism of species loss after nitrogen addition. However, solid evidence for this has been scarce. We measured the allometric size-height relationships of 25 plant species along a nitrogen addition gradient manipulated annually for eight years in a speciose alpine meadow and found that the positive relationship between species relative abundance and the height scaling exponent in natural conditions disappeared after nitrogen addition. Those species with lower height scaling exponents increased in relative abundance after nitrogen addition, thereby decreasing the community weighted mean and dispersion of the height scaling exponent and ultimately the species richness. Our results provided some unique evidence for light asymmetry induced species loss after nitrogen addition and a new insight from the perspective of allometric scaling to explain biodiversity maintenance in the face of global changes.
Collapse
Affiliation(s)
- Yao Xiao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, P. R. China
| | - Xiang Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, P. R. China
| | - Li Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, P. R. China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, P. R. China
| | - Shurong Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, 570228, P. R. China
| |
Collapse
|
28
|
Are There Differences in the Reaction of the Light-Tolerant Subgenus Pinus spp. Biomass to Climate Change as Compared to Light-Intolerant Genus Picea spp.? PLANTS 2020; 9:plants9101255. [PMID: 32977675 PMCID: PMC7598698 DOI: 10.3390/plants9101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/05/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
Currently, the problem of the impact of climate change on the productivity of forest ecosystems and their carbon-depositing capacity is far from being solved. Therefore, this paper presents the models for the stand biomass of the two-needled subgenus’ (Pinus spp.) and the genus Picea spp.’s trends along the trans-Eurasian hydrothermal gradients, designed for pure stands in a number of 2110- and 870-sample plots with Pinus and Picea correspondingly. It was found that in the case of an increase in mean winter temperatures by 1 °C, pine and spruce respond by increasing the biomass of most components, and in the case of an increase in the annual sum of precipitation by 100 mm, the total, aboveground, stem and root biomasses of pine and spruce react the same way, but crown biomass reacts in the opposite way. Therefore, all identified trends are species-specific.
Collapse
|
29
|
Patterns for Populus spp. Stand Biomass in Gradients of Winter Temperature and Precipitation of Eurasia. FORESTS 2020. [DOI: 10.3390/f11090906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Based on a generated database of 413 sample plots, with definitions of stand biomass of the genus Populus spp. in Eurasia, from France to Japan and southern China, statistically significant changes in the structure of forest stand biomass were found, with shifts in winter temperatures and average annual precipitation. When analyzing the reaction of the structure of the biomass of the genus Populus to temperature and precipitation in their transcontinental gradients, a clearly expressed positive relationship of all components of the biomass with the temperature in January is visible. Their relationship with precipitation is less clear; in warm climate zones, when precipitation increases, the biomass of all wood components decreases intensively, and in cold climate zones, this decrease is less pronounced. The foliage biomass does not increase when precipitation decreases, as is typical for wood components, but decreases. This can be explained by the specifics of the functioning of the assimilation apparatus, namely its transpiration activity when warming, and the corresponding increase in transpiration, which requires an increase in the influx of assimilates into the foliage, and the desiccation of the climate that reduces this influx of assimilates. Comparison of the obtained patterns with previously published results for other species from Eurasia showed partial or complete discrepancies, the causes of which require special physiological studies. The results obtained can be useful in the management of biosphere functions of forests, which is important in the implementation of climate stabilization measures, as well as in the validation of the results of simulation experiments to assess the carbon-deposition capacity of forests.
Collapse
|
30
|
Nagel KA, Lenz H, Kastenholz B, Gilmer F, Averesch A, Putz A, Heinz K, Fischbach A, Scharr H, Fiorani F, Walter A, Schurr U. The platform GrowScreen- Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants. PLANT METHODS 2020; 16:89. [PMID: 32582364 PMCID: PMC7310412 DOI: 10.1186/s13007-020-00631-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/15/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Root system architecture and especially its plasticity in acclimation to variable environments play a crucial role in the ability of plants to explore and acquire efficiently soil resources and ensure plant productivity. Non-destructive measurement methods are indispensable to quantify dynamic growth traits. For closing the phenotyping gap, we have developed an automated phenotyping platform, GrowScreen-Agar, for non-destructive characterization of root and shoot traits of plants grown in transparent agar medium. RESULTS The phenotyping system is capable to phenotype root systems and correlate them to whole plant development of up to 280 Arabidopsis plants within 15 min. The potential of the platform has been demonstrated by quantifying phenotypic differences within 78 Arabidopsis accessions from the 1001 genomes project. The chosen concept 'plant-to-sensor' is based on transporting plants to the imaging position, which allows for flexible experimental size and design. As transporting causes mechanical vibrations of plants, we have validated that daily imaging, and consequently, moving plants has negligible influence on plant development. Plants are cultivated in square Petri dishes modified to allow the shoot to grow in the ambient air while the roots grow inside the Petri dish filled with agar. Because it is common practice in the scientific community to grow Arabidopsis plants completely enclosed in Petri dishes, we compared development of plants that had the shoot inside with that of plants that had the shoot outside the plate. Roots of plants grown completely inside the Petri dish grew 58% slower, produced a 1.8 times higher lateral root density and showed an etiolated shoot whereas plants whose shoot grew outside the plate formed a rosette. In addition, the setup with the shoot growing outside the plate offers the unique option to accurately measure both, leaf and root traits, non-destructively, and treat roots and shoots separately. CONCLUSIONS Because the GrowScreen-Agar system can be moved from one growth chamber to another, plants can be phenotyped under a wide range of environmental conditions including future climate scenarios. In combination with a measurement throughput enabling phenotyping a large set of mutants or accessions, the platform will contribute to the identification of key genes.
Collapse
Affiliation(s)
- Kerstin A Nagel
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Henning Lenz
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bernd Kastenholz
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Frank Gilmer
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Present Address: BASF SE, 67117 Limburgerhof, Germany
| | - Andreas Averesch
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Putz
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Kathrin Heinz
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Andreas Fischbach
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Hanno Scharr
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabio Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Achim Walter
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Present Address: Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Ulrich Schurr
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
31
|
Bergès SE, Vasseur F, Bediée A, Rolland G, Masclef D, Dauzat M, van Munster M, Vile D. Natural variation of Arabidopsis thaliana responses to Cauliflower mosaic virus infection upon water deficit. PLoS Pathog 2020; 16:e1008557. [PMID: 32413076 PMCID: PMC7255604 DOI: 10.1371/journal.ppat.1008557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/28/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Plant virus pathogenicity is expected to vary with changes in the abiotic environment that affect plant physiology. Conversely, viruses can alter the host plant response to additional stimuli from antagonism to mutualism depending on the virus, the host plant and the environment. Ecological theory, specifically the CSR framework of plant strategies developed by Grime and collaborators, states that plants cannot simultaneously optimize resistance to both water deficit and pathogens. Here, we investigated the vegetative and reproductive performance of 44 natural accessions of A. thaliana originating from the Iberian Peninsula upon simultaneous exposure to soil water deficit and viral infection by the Cauliflower mosaic virus (CaMV). Following the predictions of Grime's CSR theory, we tested the hypothesis that the ruderal character of a plant genotype is positively related to its tolerance to virus infection regardless of soil water availability. Our results showed that CaMV infection decreased plant vegetative performance and annihilated reproductive success of all accessions. In general, water deficit decreased plant performance, but, despite differences in behavior, ranking of accessions tolerance to CaMV was conserved under water deficit. Ruderality, quantified from leaf traits following a previously published procedure, varied significantly among accessions, and was positively correlated with tolerance to viral infection under both well-watered and water deficit conditions, although the latter to a lesser extent. Also, in accordance with the ruderal character of the accession and previous findings, our results suggest that accession tolerance to CaMV infection is positively correlated with early flowering. Finally, plant survival to CaMV infection increased under water deficit. The complex interactions between plant, virus and abiotic environment are discussed in terms of the variation in plant ecological strategies at the intraspecific level.
Collapse
Affiliation(s)
- Sandy E. Bergès
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - François Vasseur
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
- CEFE, CNRS, EPHE, IRD, Univ Montpellier, Univ Paul Valéry Montpellier, Montpellier, France
| | - Alexis Bediée
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Gaëlle Rolland
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Diane Masclef
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | - Myriam Dauzat
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, France
| |
Collapse
|
32
|
Cheng L. Scaling Analysis of Energy in Great Lakes Water Supplies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:5071-5080. [PMID: 32207930 DOI: 10.1021/acs.est.9b05982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Resource-scale quantification of energy in water supplies is important for local-scale sustainability and for regional-, national-, and global-scale assessments of the water-energy nexus. Water supply systems within a resource region are characterized by a homogeneity in system type but a heterogeneity in system size. Size heterogeneity has traditionally imposed large challenges to energy quantification because of nonlinearities. Recently, an analytical approach for quantifying nonlinear size effects in water supplies was developed based on the complex system phenomena of skewed size abundance (decreasing abundance with increasing size in a population of systems) and allometric energy scaling (decreasing energy intensity with increasing size in an individual system). Here, building on this advance and using new, resource-scope data on Great Lakes water supplies, we explore the interaction between energy allometry and size abundance and demonstrate the application of scaling for making energy predictions in water supplies. We show that communities are driven by the allometric effect to form "large get larger" supply systems, but ultimately spatial distances impose limits on the effect, resulting in delegation of tasks to local systems to preserve energy optimality. This cross-scale, interaction perspective of scaling and the application of scaling for energy prediction together may lead to a more functional understanding of supply size abundance and more integrative quantification of supply energy and environmental impacts at the water resource scale.
Collapse
Affiliation(s)
- Likwan Cheng
- City Colleges of Chicago, 30 E. Lake Street, Chicago, Illinois 60601, United States
| |
Collapse
|
33
|
Oyiga BC, Palczak J, Wojciechowski T, Lynch JP, Naz AA, Léon J, Ballvora A. Genetic components of root architecture and anatomy adjustments to water-deficit stress in spring barley. PLANT, CELL & ENVIRONMENT 2020; 43:692-711. [PMID: 31734943 DOI: 10.1111/pce.13683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 05/26/2023]
Abstract
Roots perform vital roles for adaptation and productivity under water-deficit stress, even though their specific functions are poorly understood. In this study, the genetic control of the nodal-root architectural and anatomical response to water deficit were investigated among diverse spring barley accessions. Water deficit induced substantial variations in the nodal root traits. The cortical, stele, and total root cross-sectional areas of the main-shoot nodal roots decreased under water deficit, but increased in the tiller nodal roots. Root xylem density and arrested nodal roots increased under water deficit, with the formation of root suberization/lignification and large cortical aerenchyma. Genome-wide association study implicated 11 QTL intervals in the architectural and anatomical nodal root response to water deficit. Among them, three and four QTL intervals had strong effects across seasons and on both root architectural and anatomical traits, respectively. Genome-wide epistasis analysis revealed 44 epistatically interacting SNP loci. Further analyses showed that these QTL intervals contain important candidate genes, including ZIFL2, MATE, and PPIB, whose functions are shown to be related to the root adaptive response to water deprivation in plants. These results give novel insight into the genetic architectures of barley nodal root response to soil water deficit stress in the fields, and thus offer useful resources for root-targeted marker-assisted selection.
Collapse
Affiliation(s)
| | | | - Tobias Wojciechowski
- Forschungszentrum Jülich, Institute for Bio- and Geosciences (Plant Sciences), Bonn, Germany
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State, State College, Pennsylvania
| | - Ali A Naz
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| |
Collapse
|
34
|
Life History Variation as a Model for Understanding Trade-Offs in Plant-Environment Interactions. Curr Biol 2020; 30:R180-R189. [PMID: 32097648 DOI: 10.1016/j.cub.2020.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
All plants must allocate limited resources to survival, growth, and reproduction. In natural species, allocation strategies reflect trade-offs between survivorship risk and subsequent fitness benefits and are therefore central to a species' ecology. Artificial selection on allocation has generated high-yielding crops that often invest the bare minimum in defense or longevity. Ecological, genetic, and evolutionary analyses of plant life history - particularly with respect to longevity and resource allocation along an axis from annual to perennial species - provides a framework to evaluate trade-offs in plant-environment interactions in natural and managed systems. Recent efforts to develop new model plant systems for research and to increase agricultural resilience and efficiency by developing herbaceous perennial crops motivates our critical assessment of traditional assumptions regarding differences between annual and perennial plant species. Here, we review our present understanding of the genetic basis of physiological, developmental, and anatomical differences in wild and crop species and reach two broad conclusions. First, that perenniality and annuality should be considered syndromes comprised of many interacting traits, and that elucidating the genetic basis of these traits is required to assess models of evolution and to develop successful breeding strategies. Modern phenomic and biotechnology tools will facilitate these enquiries. Second, many classic assumptions about the difference between the two syndromes are supported by limited evidence. Throughout this Review, we highlight key knowledge gaps in the proximate and ultimate mechanisms driving life history variation, and suggest empirical approaches to parameterize trade-offs and to make progress in this critical area of direct relevance to ecology and plant performance in a changing world.
Collapse
|
35
|
Togninalli M, Seren Ü, Freudenthal JA, Monroe JG, Meng D, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. Nucleic Acids Res 2020; 48:D1063-D1068. [PMID: 31642487 PMCID: PMC7145550 DOI: 10.1093/nar/gkz925] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/26/2019] [Accepted: 10/08/2019] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.
Collapse
Affiliation(s)
- Matteo Togninalli
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ümit Seren
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Jan A Freudenthal
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - J Grey Monroe
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dazhe Meng
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
- Google, Mountain View, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Karsten Borgwardt
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University Würzburg, Würzburg, Germany
| | - Dominik G Grimm
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Bioinformatics, Straubing, Germany
| |
Collapse
|
36
|
Woodson JD. Chloroplast stress signals: regulation of cellular degradation and chloroplast turnover. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:30-37. [PMID: 31442733 DOI: 10.1016/j.pbi.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 05/11/2023]
Abstract
For 40 years, it has been known that chloroplasts signal to the nucleus and the cell to coordinate gene expression, maximize photosynthesis, and avoid stress. However, the signaling mechanisms have been challenging to uncover due to the complexity of these signals and the stresses that induce them. New research has shown that many signals are induced by singlet oxygen, a natural by-product of inefficient photosynthesis. Chloroplast singlet oxygen not only regulates nuclear gene expression, but also cellular degradation and cell death. Stressed chloroplasts also induce post-translational mechanisms, including autophagy, that allows individual chloroplasts to regulate their own degradation and turnover. Such chloroplast quality control pathways may allow cells to maintain healthy populations of chloroplasts and to avoid cumulative photo-oxidative stress in stressful environments.
Collapse
Affiliation(s)
- Jesse D Woodson
- University of Arizona, School of Plant Sciences, 303 Forbes Hall, 1140 E. South Campus Drive, Tucson, AZ 85721-0036, United States.
| |
Collapse
|
37
|
Kazakou E, Vasseur F, Sartori K, Baron E, Rowe N, Vile D. Secondary metabolites have more influence than morphophysiological traits on litter decomposability across genotypes of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 224:1532-1543. [PMID: 31179544 DOI: 10.1111/nph.15983] [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: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Although interspecific variation in plant phenotype is recognised to impact afterlife processes such as litter decomposability, it is still unclear which traits and selection pressures explain these relationships. Examining intraspecific variation is crucial to identify and compare trait effects on decomposability, and investigate the potential role of natural selection. We studied the genetic variability and relationships between decomposability, plant traits typically related to decomposability at species level (morphophysiological traits), and leaf metabolites among a set of genotypes of Arabidopsis thaliana grown under controlled conditions. We also investigated correlations between decomposability and environmental variables at genotypes collection site. We investigated the genetic architecture of decomposability with genome-wide association studies (GWAS). There was large genetic variability in decomposability that was correlated with precipitation. Morphophysiological traits had a minor effect, while secondary metabolites, especially glucosinolates, were correlated with decomposability. Consistently, GWAS suggested that genes and metabolites related to the composition of cell membranes and envelopes control the variation of decomposability across genotypes. Our study suggests that decomposability varies within species as a result of metabolic adaptation to climate. Our findings highlight that subtle variations of defence-related metabolites like glucosinolates may strongly influence after-life processes such as decomposability.
Collapse
Affiliation(s)
- Elena Kazakou
- Montpellier Supagro, Centre d'Ecologie Fonctionnelle et Evolutive (UMR CEFE), CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - François Vasseur
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
- LEPSE, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, 34060, France
| | - Kevin Sartori
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - Etienne Baron
- CEFE, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, 34090, France
| | - Nick Rowe
- AMAP, CNRS, INRA, IRD, Univ Montpellier, CIRAD, Montpellier, 34090, France
| | - Denis Vile
- LEPSE, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, 34060, France
| |
Collapse
|
38
|
Desaki Y, Takahashi S, Sato K, Maeda K, Matsui S, Yoshimi I, Miura T, Jumonji JI, Takeda J, Yashima K, Kohari M, Suenaga T, Terada H, Narisawa T, Shimizu T, Yumoto E, Miyamoto K, Narusaka M, Narusaka Y, Kaku H, Shibuya N. PUB4, a CERK1-Interacting Ubiquitin Ligase, Positively Regulates MAMP-Triggered Immunity in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:2573-2583. [PMID: 31368495 DOI: 10.1093/pcp/pcz151] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Lysin motif (LysM) receptor-like kinase CERK1 is a co-receptor essential for plant immune responses against carbohydrate microbe-associated molecular patterns (MAMPs). Concerning the immediate downstream signaling components of CERK1, receptor-like cytoplasmic kinases such as PBL27 and other RLCK VII members have been reported to regulate immune responses positively. In this study, we report that a novel CERK1-interacting E3 ubiquitin ligase, PUB4, is also involved in the regulation of MAMP-triggered immune responses. Knockout of PUB4 resulted in the alteration of chitin-induced defense responses, indicating that PUB4 positively regulates reactive oxygen species generation and callose deposition but negatively regulates MAPK activation and defense gene expression. On the other hand, detailed analyses of a double knockout mutant of pub4 and sid2, a mutant of salicylic acid (SA) synthesis pathway, showed that the contradictory phenotype of the pub4 mutant was actually caused by abnormal accumulation of SA in this mutant and that PUB4 is a positive regulator of immune responses. The present and recent findings on the role of PUB4 indicate that PUB4 is a unique E3 ubiquitin ligase involved in the regulation of both plant immunity and growth/development.
Collapse
Affiliation(s)
- Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Shohei Takahashi
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kenta Sato
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kanako Maeda
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Saki Matsui
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Ikuya Yoshimi
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Takaki Miura
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Jun-Ichi Jumonji
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Jun Takeda
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Kohei Yashima
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masaki Kohari
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Takayoshi Suenaga
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Hayato Terada
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Tomoko Narisawa
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Takeo Shimizu
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Emi Yumoto
- Advanced Instrumental Analysis Center, Teikyo University, Utsunomiya, Tochigi, Japan
| | - Koji Miyamoto
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, Utsunomiya, Tochigi, Japan
| | - Mari Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Okayama, Japan
| | - Yoshihiro Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Okayama, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| |
Collapse
|
39
|
Rudgers JA, Hallmark A, Baker SR, Baur L, Hall KM, Litvak ME, Muldavin EH, Pockman WT, Whitney KD. Sensitivity of dryland plant allometry to climate. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13463] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | - Alesia Hallmark
- Department of Biology University of New Mexico Albuquerque NM USA
| | | | - Lauren Baur
- Department of Biology University of New Mexico Albuquerque NM USA
| | | | - Marcy E. Litvak
- Department of Biology University of New Mexico Albuquerque NM USA
| | | | | | | |
Collapse
|
40
|
Sartori K, Vasseur F, Violle C, Baron E, Gerard M, Rowe N, Ayala-Garay O, Christophe A, Jalón LGD, Masclef D, Harscouet E, Granado MDR, Chassagneux A, Kazakou E, Vile D. Leaf economics and slow-fast adaptation across the geographic range of Arabidopsis thaliana. Sci Rep 2019; 9:10758. [PMID: 31341185 PMCID: PMC6656729 DOI: 10.1038/s41598-019-46878-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 07/01/2019] [Indexed: 11/08/2022] Open
Abstract
Life history strategies of most organisms are constrained by resource allocation patterns that follow a 'slow-fast continuum'. It opposes slow growing and long-lived organisms with late investment in reproduction to those that grow faster, have earlier and larger reproductive effort and a short longevity. In plants, the Leaf Economics Spectrum (LES) depicts a leaf-level trade-off between the rate of carbon assimilation and leaf lifespan, as stressed in functional ecology from interspecific comparative studies. However, it is still unclear how the LES is connected to the slow-fast syndrome. Interspecific comparisons also impede a deep exploration of the linkage between LES variation and adaptation to climate. Here, we measured growth, morpho-physiological and life-history traits, at both the leaf and whole-plant levels, in 378 natural accessions of Arabidopsis thaliana. We found that the LES is tightly linked to variation in whole-plant functioning, and aligns with the slow-fast continuum. A genetic analysis further suggested that phenotypic differentiation results from the selection of different slow-fast strategies in contrasted climates. Slow growing and long-lived plants were preferentially found in cold and arid habitats while fast growing and short-lived ones in more favorable habitats. Our findings shed light on the role of the slow-fast continuum for plant adaptation to climate. More broadly, they encourage future studies to bridge functional ecology, genetics and evolutionary biology to improve our understanding of plant adaptation to environmental changes.
Collapse
Affiliation(s)
- Kevin Sartori
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - François Vasseur
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
- Univ Montpellier, INRA, Montpellier SupAgro, LEPSE, Montpellier, France
| | - Cyrille Violle
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Etienne Baron
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Marianne Gerard
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Nick Rowe
- Univ Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier, France
| | - Oscar Ayala-Garay
- Univ Montpellier, INRA, Montpellier SupAgro, LEPSE, Montpellier, France
- Programa de Recursos Genéticos y Productividad (RGP)-Fisiología Vegetal, Colegio de Postgraduados, 56230, Texcoco, Mexico
| | - Ananda Christophe
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Laura Garcia de Jalón
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Diane Masclef
- Univ Montpellier, INRA, Montpellier SupAgro, LEPSE, Montpellier, France
| | - Erwan Harscouet
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Maria Del Rey Granado
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Agathe Chassagneux
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
- Office National de la Chasse et de la Faune sauvage, DRE Unité, Ongulés sauvages, Birieux, France
| | - Elena Kazakou
- Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
- Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Denis Vile
- Univ Montpellier, INRA, Montpellier SupAgro, LEPSE, Montpellier, France
| |
Collapse
|
41
|
Kumordzi BB, Aubin I, Cardou F, Shipley B, Violle C, Johnstone J, Anand M, Arsenault A, Bell FW, Bergeron Y, Boulangeat I, Brousseau M, De Grandpré L, Delagrange S, Fenton NJ, Gravel D, Macdonald SE, Hamel B, Higelin M, Hébert F, Isabel N, Mallik A, McIntosh AC, McLaren JR, Messier C, Morris D, Thiffault N, Tremblay J, Munson AD. Geographic scale and disturbance influence intraspecific trait variability in leaves and roots of North American understorey plants. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13402] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Bright B. Kumordzi
- Centre d’étude de la forêt, Département des sciences du bois et de la forêt Université Laval Québec QC Canada
| | - Isabelle Aubin
- Great Lakes Forestry Centre, Canadian Forest Service Natural Resources Canada Sault Ste Marie ON Canada
| | - Françoise Cardou
- Great Lakes Forestry Centre, Canadian Forest Service Natural Resources Canada Sault Ste Marie ON Canada
- Département de biologie Université de Sherbrooke Sherbrooke QC Canada
| | - Bill Shipley
- Département de biologie Université de Sherbrooke Sherbrooke QC Canada
| | - Cyrille Violle
- CEFE, UMR 5175 CNRS – Université de Montpellier – Université Paul‐Valéry Montpellier – EPHE Montpellier France
| | - Jill Johnstone
- Department of Biology University of Saskatchewan Saskatoon SK Canada
| | - Madhur Anand
- School of Environmental Sciences University of Guelph Guelph ON Canada
| | - André Arsenault
- Atlantic Forestry Centre, Canadian Forest Service and School of Science and the Environment Memorial University of Newfoundland Corner Brook NL Canada
| | - F. Wayne Bell
- Ontario Forest Research Institute Ontario Ministry of Natural Resources and Forestry Sault Ste Marie ON Canada
| | - Yves Bergeron
- Institut de recherche sur les forêts Université du Québec en Abitibi‐Témiscamingue Rouyn‐Noranda QC Canada
| | | | - Maxime Brousseau
- Département de biologie and Centre d'étude de la forêt Université Laval Québec QC Canada
| | - Louis De Grandpré
- Laurentian Forestry Centre, Canadian Forest Service Natural Resources Canada Québec QC Canada
| | - Sylvain Delagrange
- Institut des Sciences de la Forêt Tempérée Université du Québec en Outaouais Ripon QC Canada
| | - Nicole J. Fenton
- Institut de recherche sur les forêts Université du Québec en Abitibi‐Témiscamingue Rouyn‐Noranda QC Canada
| | - Dominique Gravel
- Département de biologie Université de Sherbrooke Sherbrooke QC Canada
| | - S. Ellen Macdonald
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - Benoit Hamel
- Great Lakes Forestry Centre, Canadian Forest Service Natural Resources Canada Sault Ste Marie ON Canada
| | - Morgane Higelin
- Institut de recherche sur les forêts Université du Québec en Abitibi‐Témiscamingue Rouyn‐Noranda QC Canada
| | - François Hébert
- Direction de la recherche forestière Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Nathalie Isabel
- Laurentian Forestry Centre, Canadian Forest Service Natural Resources Canada Québec QC Canada
| | - Azim Mallik
- Department of Biology Lakehead University Thunder Bay ON Canada
| | | | - Jennie R. McLaren
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Christian Messier
- Institut des Sciences de la Forêt Tempérée Université du Québec en Outaouais Ripon QC Canada
- Centre d'Étude de la Forêt Université du Québec à Montréal Montréal QC Canada
| | - Dave Morris
- Centre for Northern Forest Ecosystem Research Ontario Ministry of Natural Resources and Forestry Thunder Bay ON Canada
| | - Nelson Thiffault
- Centre d’étude de la forêt, Département des sciences du bois et de la forêt Université Laval Québec QC Canada
- Canadian Wood Fibre Centre Natural Resources Canada Québec QC Canada
| | - Jean‐Pierre Tremblay
- Département de biologie and Centre d'étude de la forêt Université Laval Québec QC Canada
| | - Alison D. Munson
- Centre d’étude de la forêt, Département des sciences du bois et de la forêt Université Laval Québec QC Canada
| |
Collapse
|
42
|
Vasseur F, Fouqueau L, de Vienne D, Nidelet T, Violle C, Weigel D. Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLoS Biol 2019; 17:e3000214. [PMID: 31017902 PMCID: PMC6481775 DOI: 10.1371/journal.pbio.3000214] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
Collapse
Affiliation(s)
- François Vasseur
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR759, Montpellier, France
| | - Louise Fouqueau
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Dominique de Vienne
- GQE–Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Univ Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
43
|
Takou M, Wieters B, Kopriva S, Coupland G, Linstädter A, De Meaux J. Linking genes with ecological strategies in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1141-1151. [PMID: 30561727 PMCID: PMC6382341 DOI: 10.1093/jxb/ery447] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 05/22/2023]
Abstract
Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.
Collapse
Affiliation(s)
| | | | | | - George Coupland
- Max Planck Institute of Plant Breeding Research, Cologne, Germany
| | - Anja Linstädter
- Institute of Botany, University of Cologne, Germany
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Germany
| | | |
Collapse
|
44
|
Vasseur F, Sartori K, Baron E, Fort F, Kazakou E, Segrestin J, Garnier E, Vile D, Violle C. Climate as a driver of adaptive variations in ecological strategies in Arabidopsis thaliana. ANNALS OF BOTANY 2018; 122:935-945. [PMID: 30256896 PMCID: PMC6266113 DOI: 10.1093/aob/mcy165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/16/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The CSR classification categorizes plants as stress tolerators (S), ruderals (R) and competitors (C). Initially proposed as a general framework to describe ecological strategies across species, this scheme has recently been used to investigate the variation of strategies within species. For instance, ample variation along the S-R axis was found in Arabidopsis thaliana, with stress-tolerator accessions predominating in hot and dry regions, which was interpreted as a sign of functional adaptation to climate within the species. METHODS In this study the range of CSR strategies within A. thaliana was evaluated across 426 accessions originating from North Africa to Scandinavia. A position in the CSR strategy space was allocated for every accession based on three functional traits: leaf area, leaf dry matter content (LDMC) and specific leaf area (SLA). Results were related to climate at origin and compared with a previous study performed on the same species. Furthermore, the role of natural selection in phenotypic differentiation between lineages was investigated with QST-FST comparisons, using the large amount of genetic information available for this species. KEY RESULTS Substantial variation in ecological strategies along the S-R axis was found in A. thaliana. By contrast with previous findings, stress-tolerator accessions predominated in cold climates, notably Scandinavia, where late flowering was associated with traits related to resource conservation, such as high LDMC and low SLA. Because of trait plasticity, variations in CSR classification in relation to growth conditions were also observed for the same genotypes. CONCLUSIONS There is a latitudinal gradient of ecological strategies in A. thaliana as a result of within-species adaptation to climate. Our study also underlines the importance of growth conditions and of the methodology used for trait measurement, notably age versus stage measurement, to infer the strength and direction of trait-environment relationships. This highlights the potential and limitations of the CSR classification in explaining functional adaptation to the environment.
Collapse
Affiliation(s)
- François Vasseur
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR, Montpellier, France
- For correspondence. E-mail
| | - Kevin Sartori
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Etienne Baron
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Florian Fort
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Elena Kazakou
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Jules Segrestin
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Eric Garnier
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| | - Denis Vile
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, Montpellier SupAgro, Université de Montpellier, Université Paul Valéry Montpellier, EPHE, Montpellier, France
| |
Collapse
|
45
|
Vasseur F, Bresson J, Wang G, Schwab R, Weigel D. Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana. PLANT METHODS 2018; 14:63. [PMID: 30065776 PMCID: PMC6060534 DOI: 10.1186/s13007-018-0331-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/23/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND The model species Arabidopsis thaliana has extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits. However, the cost of equipment and software required for high-throughput phenotyping is often a bottleneck for large-scale studies, such as mutant screening or quantitative genetics analyses. Simple tools are needed for the measurement of fitness-related traits, like relative growth rate and fruit production, without investment in expensive infrastructures. Here, we describe methods that enable the estimation of biomass accumulation and fruit number from the analysis of rosette and inflorescence images taken with a regular camera. RESULTS We developed two models to predict plant dry mass and fruit number from the parameters extracted with the analysis of rosette and inflorescence images. Predictive models were trained by sacrificing growing individuals for dry mass estimation, and manually measuring a fraction of individuals for fruit number at maturity. Using a cross-validation approach, we showed that quantitative parameters extracted from image analysis predicts more 90% of both plant dry mass and fruit number. When used on 451 natural accessions, the method allowed modeling growth dynamics, including relative growth rate, throughout the life cycle of various ecotypes. Estimated growth-related traits had high heritability (0.65 < H2 < 0.93), as well as estimated fruit number (H2 = 0.68). In addition, we validated the method for estimating fruit number with rev5, a mutant with increased flower abortion. CONCLUSIONS The method we propose here is an application of automated computerization of plant images with ImageJ, and subsequent statistical modeling in R. It allows plant biologists to measure growth dynamics and fruit number in hundreds of individuals with simple computing steps that can be repeated and adjusted to a wide range of laboratory conditions. It is thus a flexible toolkit for the measurement of fitness-related traits in large populations of a model species.
Collapse
Affiliation(s)
- François Vasseur
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Justine Bresson
- Center for Plant Molecular Biology (ZMBP), General Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - George Wang
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|
46
|
Salguero‐Gómez R, Violle C, Gimenez O, Childs D, Fox C. Delivering the promises of trait-based approaches to the needs of demographic approaches, and vice versa. Funct Ecol 2018; 32:1424-1435. [PMID: 30034074 PMCID: PMC6049886 DOI: 10.1111/1365-2435.13148] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/22/2018] [Indexed: 11/28/2022]
Abstract
Few facets of biology vary more than functional traits and life-history traits. To explore this vast variation, functional ecologists and population ecologists have developed independent approaches that identify the mechanisms behind and consequences of trait variation.Collaborative research between researchers using trait-based and demographic approaches remains scarce. We argue that this is a missed opportunity, as the strengths of both approaches could help boost the research agendas of functional ecology and population ecology.This special feature, which spans three journals of the British Ecological Society due to its interdisciplinary nature, showcases state-of-the-art research applying trait-based and demographic approaches to examine relationships between organismal function, life history strategies and population performance across multiple kingdoms. Examples include the exploration of how functional trait × environment interactions affect vital rates and thus explain population trends and species occurrence; the coordination of seed traits and dispersal ability with the pace of life in plants; the incorporation of functional traits in dynamic energy budget models; or the discovery of linkages between microbial functional traits and the fast-slow continuum.Despite their historical isolation, collaborative work between functional ecologists and population ecologists could unlock novel research pathways. We call for an integrative research agenda to evaluate which and when traits are functional, as well as their ability to describe and predict life history strategies and population dynamics. We highlight promising, complementary research avenues to overcome current limitations. These include a more explicit linkage of selection gradients in the context of functional trait-vital rate relationships, and the implementation of standardised protocols to track changes in traits and vital rates over time at the same location and individuals, thus allowing for the explicit incorporation of trade-offs in analyses of covariation of functional traits and life-history traits.
Collapse
Affiliation(s)
- Roberto Salguero‐Gómez
- Department of ZoologyUniversity of OxfordOxfordUK
- Evolutionary Biodemography LaboratoryMax Planck Institute for Demographic ResearchRostockGermany
- Centre for Biodiversity and Conservation ScienceUniversity of QueenslandSt LuciaQldAustralia
| | - Cyrille Violle
- CEFE, CNRSUniv MontpellierUniv Paul Valéry Montpellier 3, EPHE, IRDMontpellierFrance
| | - Olivier Gimenez
- CEFE, CNRSUniv MontpellierUniv Paul Valéry Montpellier 3, EPHE, IRDMontpellierFrance
| | - Dylan Childs
- Department of Animal & Plant SciencesThe University of SheffieldSheffieldUK
| | | |
Collapse
|
47
|
Vasseur F, Bresson J, Wang G, Schwab R, Weigel D. Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana. PLANT METHODS 2018. [PMID: 30065776 DOI: 10.1101/208512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND The model species Arabidopsis thaliana has extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits. However, the cost of equipment and software required for high-throughput phenotyping is often a bottleneck for large-scale studies, such as mutant screening or quantitative genetics analyses. Simple tools are needed for the measurement of fitness-related traits, like relative growth rate and fruit production, without investment in expensive infrastructures. Here, we describe methods that enable the estimation of biomass accumulation and fruit number from the analysis of rosette and inflorescence images taken with a regular camera. RESULTS We developed two models to predict plant dry mass and fruit number from the parameters extracted with the analysis of rosette and inflorescence images. Predictive models were trained by sacrificing growing individuals for dry mass estimation, and manually measuring a fraction of individuals for fruit number at maturity. Using a cross-validation approach, we showed that quantitative parameters extracted from image analysis predicts more 90% of both plant dry mass and fruit number. When used on 451 natural accessions, the method allowed modeling growth dynamics, including relative growth rate, throughout the life cycle of various ecotypes. Estimated growth-related traits had high heritability (0.65 < H2 < 0.93), as well as estimated fruit number (H2 = 0.68). In addition, we validated the method for estimating fruit number with rev5, a mutant with increased flower abortion. CONCLUSIONS The method we propose here is an application of automated computerization of plant images with ImageJ, and subsequent statistical modeling in R. It allows plant biologists to measure growth dynamics and fruit number in hundreds of individuals with simple computing steps that can be repeated and adjusted to a wide range of laboratory conditions. It is thus a flexible toolkit for the measurement of fitness-related traits in large populations of a model species.
Collapse
Affiliation(s)
- François Vasseur
- 1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Justine Bresson
- 2Center for Plant Molecular Biology (ZMBP), General Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - George Wang
- 1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- 1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- 1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|