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Przybylska MS, Violle C, Vile D, Scheepens JF, Munoz F, Tenllado Á, Vinyeta M, Le Roux X, Vasseur F. Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 243:620-635. [PMID: 38812269 DOI: 10.1111/nph.19870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.
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Affiliation(s)
- Maria Stefania Przybylska
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
| | - J F Scheepens
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - François Munoz
- LiPhy, Université Grenoble-Alpes, 38041, Grenoble, France
| | - Álvaro Tenllado
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - Mariona Vinyeta
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Xavier Le Roux
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
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2
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Minadakis N, Kaderli L, Horvath R, Bourgeois Y, Xu W, Thieme M, Woods DP, Roulin AC. Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon. Genetics 2024; 227:iyae042. [PMID: 38504651 DOI: 10.1093/genetics/iyae042] [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: 01/12/2024] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.
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Affiliation(s)
- Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Lars Kaderli
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Robert Horvath
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34 000 Montpellier, France
| | - Wenbo Xu
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Michael Thieme
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Daniel P Woods
- Department of Plant Sciences, University of California-Davis, 104 Robbins Hall, Davis, CA 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
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Takou M, Bellis ES, Lasky JR. Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591174. [PMID: 38712066 PMCID: PMC11071634 DOI: 10.1101/2024.04.25.591174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The evolution of gene expression responses are a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis- regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learn de novo cis- regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, DEGs between specific environments can be predicted based on variation in cis- regulatory sequences, although more information needs to be incorporated and better models may be required.
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4
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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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Bravo-Vázquez LA, Méndez-García A, Chamu-García V, Rodríguez AL, Bandyopadhyay A, Paul S. The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research. PLANTA 2023; 259:32. [PMID: 38153530 DOI: 10.1007/s00425-023-04303-z] [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: 05/28/2023] [Accepted: 11/25/2023] [Indexed: 12/29/2023]
Abstract
MAIN CONCLUSION CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Andrea Méndez-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Verenice Chamu-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Puebla, Atlixcáyotl 5718, Reserva Territorial Atlixcáyotl, 72453, Puebla, Mexico
| | - Alma L Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Anindya Bandyopadhyay
- International Rice Research Institute, 4031, Manila, Philippines.
- Reliance Industries Ltd., Navi Mumbai, Maharashtra, 400701, India.
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico.
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6
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Montazeaud G, Helleu Q, Wuest SE, Keller L. Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana. Nat Ecol Evol 2023; 7:1878-1891. [PMID: 37749402 DOI: 10.1038/s41559-023-02189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023]
Abstract
The phenotype of an individual can be affected by the genes of its conspecifics through indirect genetic effects (IGEs). IGEs have been studied across different organisms including wild and domesticated animals and plants, but little is known about their genetic architecture. Here, in a large-scale intraspecific interaction experiment, we show that the contribution of IGEs to the biomass variation of Arabidopsis thaliana is comparable to values classically reported in animals. Moreover, we identify 11 loci explaining 85.1% of the variability in IGEs. We find that positive IGE alleles (that is, those with positive effects on neighbour biomass) occur both in relict accessions from southern Eurasia and in post-glacial colonizers from northern Scandinavia, and that they are likely to have two divergent origins: for nine loci, they evolved in the post-glacial colonizers independently from the relicts, while the two others were introgressed in the post-glacial colonizer from the relicts. Finally, we find that variation in IGEs probably reflects divergent adaptations to the contrasting environments of the edges and the centre of the native range of the species. These findings reveal a surprisingly tractable genetic basis of IGEs in A. thaliana that is shaped by the ecology and the demographic history of the species.
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Affiliation(s)
- Germain Montazeaud
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS UMR7196, INSERM U1154, Paris, France
| | - Samuel E Wuest
- Group Breeding Research, Division Plant Breeding, Agroscope, Wädenswil, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Social Evolution Unit, Chesières, Switzerland.
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7
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Atamian HS, Funk JL. Physiological and transcriptomic responses of two Artemisia californica populations to drought: implications for restoring drought-resilient native communities. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
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8
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Cock JM. The model system Ectocarpus: Integrating functional genomics into brown algal research. JOURNAL OF PHYCOLOGY 2023; 59:4-8. [PMID: 36477437 DOI: 10.1111/jpy.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Affiliation(s)
- J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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9
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McMinn R, Salmela MJ, Weinig C. Naturally segregating genetic variation in circadian period exhibits a regional elevational and climatic cline. PLANT, CELL & ENVIRONMENT 2022; 45:2696-2707. [PMID: 35686466 DOI: 10.1111/pce.14377] [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: 10/04/2021] [Revised: 05/15/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Circadian clocks confer adaptation to predictable 24-h fluctuations in the exogenous environment, but it has yet to be determined what ecological factors maintain natural genetic variation in endogenous circadian period outside of the hypothesized optimum of 24 h. We estimated quantitative genetic variation in circadian period in leaf movement in 30 natural populations of the Arabidopsis relative Boechera stricta sampled within only 1° of latitude but across an elevation gradient spanning 2460-3300 m in the Rocky Mountains. Measuring ~3800 plants from 473 maternal families (7-20 per population), we found that genetic variation was of similar magnitude among versus within populations, with population means varying between 21.9 and 24.9 h and maternal family means within populations varying by up to ~6 h. After statistically accounting for spatial autocorrelation at a habitat extreme, we found that elevation explained a significant proportion of genetic variation in the circadian period, such that higher-elevation populations had shorter mean period lengths and reduced intrapopulation ranges. Environmental data indicate that these spatial trends could be related to steep regional climatic gradients in temperature, precipitation, and their intra-annual variability. Our findings suggest that spatially fine-grained environmental heterogeneity contributes to naturally occurring genetic variation in circadian traits in wild populations.
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Affiliation(s)
- Rob McMinn
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | | | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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10
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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.
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11
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Clauw P, Kerdaffrec E, Gunis J, Reichardt-Gomez I, Nizhynska V, Koemeda S, Jez J, Nordborg M. Locally adaptive temperature response of vegetative growth in Arabidopsis thaliana. eLife 2022; 11:77913. [PMID: 35904422 PMCID: PMC9337855 DOI: 10.7554/elife.77913] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/13/2022] [Indexed: 02/06/2023] Open
Abstract
We investigated early vegetative growth of natural Arabidopsis thaliana accessions in cold, nonfreezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes. We found that accessions from northern latitudes produced larger seedlings than accessions from southern latitudes, partly as a result of larger seed size. However, their subsequent vegetative growth when exposed to colder temperatures was slower. The difference was too large to be explained by random population differentiation, and is thus suggestive of local adaptation, a notion that is further supported by substantial transcriptome and metabolome changes in northern accessions. We hypothesize that the reduced growth of northern accessions is an adaptive response and a consequence of reallocating resources toward cold acclimation and winter survival.
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Affiliation(s)
- Pieter Clauw
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Envel Kerdaffrec
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joanna Gunis
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | | | - Viktoria Nizhynska
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Stefanie Koemeda
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - Jakub Jez
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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12
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Vasseur F, Cornet D, Beurier G, Messier J, Rouan L, Bresson J, Ecarnot M, Stahl M, Heumos S, Gérard M, Reijnen H, Tillard P, Lacombe B, Emanuel A, Floret J, Estarague A, Przybylska S, Sartori K, Gillespie LM, Baron E, Kazakou E, Vile D, Violle C. A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2022; 13:836488. [PMID: 35668791 PMCID: PMC9163986 DOI: 10.3389/fpls.2022.836488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 05/31/2023]
Abstract
The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.
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Affiliation(s)
| | - Denis Cornet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Grégory Beurier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Julie Messier
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Justine Bresson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mark Stahl
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Quantitative Biology Center (QBiC), University of Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Marianne Gérard
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hans Reijnen
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pascal Tillard
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Amélie Emanuel
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Justine Floret
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kevin Sartori
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Etienne Baron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Elena Kazakou
- CEFE, Univ Montpellier, CNRS, EPHE, Institut Agro, IRD, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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13
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Morón-García O, Garzón-Martínez GA, Martínez-Martín MJP, Brook J, Corke FMK, Doonan JH, Camargo Rodríguez AV. Genetic architecture of variation in Arabidopsis thaliana rosettes. PLoS One 2022; 17:e0263985. [PMID: 35171969 PMCID: PMC8849614 DOI: 10.1371/journal.pone.0263985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/01/2022] [Indexed: 12/04/2022] Open
Abstract
Rosette morphology across Arabidopsis accessions exhibits considerable variation. Here we report a high-throughput phenotyping approach based on automatic image analysis to quantify rosette shape and dissect the underlying genetic architecture. Shape measurements of the rosettes in a core set of Recombinant Inbred Lines from an advanced mapping population (Multiparent Advanced Generation Inter-Cross or MAGIC) derived from inter-crossing 19 natural accessions. Image acquisition and analysis was scaled to extract geometric descriptors from time stamped images of growing rosettes. Shape analyses revealed heritable morphological variation at early juvenile stages and QTL mapping resulted in over 116 chromosomal regions associated with trait variation within the population. Many QTL linked to variation in shape were located near genes related to hormonal signalling and signal transduction pathways while others are involved in shade avoidance and transition to flowering. Our results suggest rosette shape arises from modular integration of sub-organ morphologies and can be considered a functional trait subjected to selective pressures of subsequent morphological traits. On an applied aspect, QTLs found will be candidates for further research on plant architecture.
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Affiliation(s)
- Odín Morón-García
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Gina A. Garzón-Martínez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - M. J. Pilar Martínez-Martín
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jason Brook
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Fiona M. K. Corke
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
| | - Anyela V. Camargo Rodríguez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
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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.
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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
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15
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Libourel C, Baron E, Lenglet J, Amsellem L, Roby D, Roux F. The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods. FRONTIERS IN PLANT SCIENCE 2021; 12:741122. [PMID: 34899774 PMCID: PMC8656689 DOI: 10.3389/fpls.2021.741122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.
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Affiliation(s)
- Cyril Libourel
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Etienne Baron
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Juliana Lenglet
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Laurent Amsellem
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
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Kinmonth-Schultz H, Lewandowska-Sabat A, Imaizumi T, Ward JK, Rognli OA, Fjellheim S. Flowering Times of Wild Arabidopsis Accessions From Across Norway Correlate With Expression Levels of FT, CO, and FLC Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:747740. [PMID: 34790213 PMCID: PMC8591261 DOI: 10.3389/fpls.2021.747740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/30/2021] [Indexed: 06/12/2023]
Abstract
Temperate species often require or flower most rapidly in the long daylengths, or photoperiods, experienced in summer or after prolonged periods of cold temperatures, referred to as vernalization. Yet, even within species, plants vary in the degree of responsiveness to these cues. In Arabidopsis thaliana, CONSTANS (CO) and FLOWERING LOCUS C (FLC) genes are key to photoperiod and vernalization perception and antagonistically regulate FLOWERING LOCUS T (FT) to influence the flowering time of the plants. However, it is still an open question as to how these genes vary in their interactions among wild accessions with different flowering behaviors and adapted to different microclimates, yet this knowledge could improve our ability to predict plant responses in variable natural conditions. To assess the relationships among these genes and to flowering time, we exposed 10 winter-annual Arabidopsis accessions from throughout Norway, ranging from early to late flowering, along with two summer-annual accessions to 14 weeks of vernalization and either 8- or 19-h photoperiods to mimic Norwegian climate conditions, then assessed gene expression levels 3-, 5-, and 8-days post vernalization. CO and FLC explained both FT levels and flowering time (days) but not rosette leaf number at flowering. The correlation between FT and flowering time increased over time. Although vernalization suppresses FLC, FLC was high in the late-flowering accessions. Across accessions, FT was expressed only at low FLC levels and did not respond to CO in the late-flowering accessions. We proposed that FT may only be expressed below a threshold value of FLC and demonstrated that these three genes correlated to flowering times across genetically distinct accessions of Arabidopsis.
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
| | | | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Joy K. Ward
- College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Odd Arne Rognli
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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18
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Burnette TE, Eckhart VM. Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Are trait combinations facilitated, independent, or constrained? AMERICAN JOURNAL OF BOTANY 2021; 108:309-319. [PMID: 33524185 PMCID: PMC7986167 DOI: 10.1002/ajb2.1607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/14/2020] [Indexed: 05/17/2023]
Abstract
PREMISE Whether drought-adaptation mechanisms tend to evolve together, evolve independently, or evolve constrained by genetic architecture is incompletely resolved, particularly for water-relations traits besides gas exchange. We addressed this issue in two subspecies of Clarkia xantiana (Onagraceae), California winter annuals that separated approximately 65,000 years ago and are adapted, partly by differences in flowering time, to native ranges differing in precipitation. METHODS In these subspecies and in recombinant inbred lines (RILs) from a cross between them, we scored traits related to drought adaptation (timing of seed germination and of flowering, succulence, pressure-volume curve variables) in common environments. RESULTS The subspecies native to more arid environments (parviflora) exhibited slower seed germination in saturated conditions, earlier flowering, and greater succulence, likely indicating superior drought avoidance, drought escape, and dehydration resistance via water storage. The other subspecies (xantiana) had lower osmotic potential at full turgor and lower water potential at turgor loss, implying superior dehydration tolerance. Genetic correlations among RILs suggest facilitated evolution of some trait combinations and independence of others. Where genetic correlations exist, subspecies differences fell along them, with the exception of differences in succulence and turgor loss point. In that case, subspecies difference overcame genetic correlations, possibly reflecting strong selection and/or antagonistic genetic correlations with other traits. CONCLUSIONS Clarkia xantiana subspecies' differ in multiple mechanisms of drought adaptation. Genetic architecture generally does not seem to have constrained the evolution of these mechanisms, and it may have facilitated the evolution of some of trait combinations.
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Affiliation(s)
- Timothy E. Burnette
- Division of Biological SciencesUniversity of MontanaMissoulaMT59802USA
- Department of BiologyGrinnell CollegeGrinnellIA50112USA
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19
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Burnette TE, Eckhart VM. Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Are trait combinations facilitated, independent, or constrained? AMERICAN JOURNAL OF BOTANY 2021; 108:309-319. [PMID: 33524185 DOI: 10.5061/dryad.k3j9kd55k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/14/2020] [Indexed: 05/28/2023]
Abstract
PREMISE Whether drought-adaptation mechanisms tend to evolve together, evolve independently, or evolve constrained by genetic architecture is incompletely resolved, particularly for water-relations traits besides gas exchange. We addressed this issue in two subspecies of Clarkia xantiana (Onagraceae), California winter annuals that separated approximately 65,000 years ago and are adapted, partly by differences in flowering time, to native ranges differing in precipitation. METHODS In these subspecies and in recombinant inbred lines (RILs) from a cross between them, we scored traits related to drought adaptation (timing of seed germination and of flowering, succulence, pressure-volume curve variables) in common environments. RESULTS The subspecies native to more arid environments (parviflora) exhibited slower seed germination in saturated conditions, earlier flowering, and greater succulence, likely indicating superior drought avoidance, drought escape, and dehydration resistance via water storage. The other subspecies (xantiana) had lower osmotic potential at full turgor and lower water potential at turgor loss, implying superior dehydration tolerance. Genetic correlations among RILs suggest facilitated evolution of some trait combinations and independence of others. Where genetic correlations exist, subspecies differences fell along them, with the exception of differences in succulence and turgor loss point. In that case, subspecies difference overcame genetic correlations, possibly reflecting strong selection and/or antagonistic genetic correlations with other traits. CONCLUSIONS Clarkia xantiana subspecies' differ in multiple mechanisms of drought adaptation. Genetic architecture generally does not seem to have constrained the evolution of these mechanisms, and it may have facilitated the evolution of some of trait combinations.
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Affiliation(s)
- Timothy E Burnette
- Division of Biological Sciences, University of Montana, Missoula, MT, 59802, USA
- Department of Biology, Grinnell College, Grinnell, IA, 50112, USA
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20
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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.
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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:
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Matsusaka D, Filiault D, Sanchez DH, Botto JF. Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia. FRONTIERS IN PLANT SCIENCE 2021; 12:677728. [PMID: 34367202 PMCID: PMC8343176 DOI: 10.3389/fpls.2021.677728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/22/2021] [Indexed: 05/15/2023]
Abstract
Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.
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Affiliation(s)
- Daniel Matsusaka
- IFEVA, UBA, CONICET, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniele Filiault
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Diego H. Sanchez
- IFEVA, UBA, CONICET, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier F. Botto
- IFEVA, UBA, CONICET, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Javier F. Botto,
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Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:2526-2534. [PMID: 31964817 PMCID: PMC7007534 DOI: 10.1073/pnas.1912451117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The seasonal timing of seed germination is critical for plant fitness in different climates. To germinate at the right time of year, seeds respond to seasonal environmental cues, such as cold temperatures. We characterized genetic variation in seed dormancy responses to cold across the geographic range of a widespread annual plant. Induction of secondary seed dormancy during winter conditions (which restricts germination to autumn) was positively correlated with flowering time, constructing winter and spring seasonal life-history strategies. Variation in seed chilling responses was strongly associated with functional variants of a known dormancy gene. These variants showed evidence of ancient diversification associated with Pleistocene glacial cycles, and were associated with climate gradients across the species’ geographical range. The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.
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Honjo MN, Kudoh H. Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AOB PLANTS 2019; 11:plz076. [PMID: 31832127 PMCID: PMC6899346 DOI: 10.1093/aobpla/plz076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/26/2019] [Indexed: 05/21/2023]
Abstract
Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
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Affiliation(s)
- Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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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: 21] [Impact Index Per Article: 4.2] [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.
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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
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