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de la Mata R, Mollá-Morales A, Méndez-Vigo B, Torres-Pérez R, Oliveros JC, Gómez R, Marcer A, Castilla AR, Nordborg M, Alonso-Blanco C, Picó FX. Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity. BMC Ecol Evol 2024; 24:56. [PMID: 38702598 PMCID: PMC11067129 DOI: 10.1186/s12862-024-02246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. RESULTS Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. CONCLUSIONS Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.
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Affiliation(s)
- Raul de la Mata
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
- Faculty of Forestry, Institute of Dehesa Research (INDEHESA), Universidad de Extremadura, 10600, Plasencia, Spain
| | | | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rocío Gómez
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
| | - Arnald Marcer
- CREAF, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
| | - Antonio R Castilla
- Department of Plant Biology, Ecology, and Evolution, College of Arts and Sciences, Oklahoma State University, Stillwater, OK, 74078-3031, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain.
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Fuster-Pons A, Murillo-Sánchez A, Méndez-Vigo B, Marcer A, Pieper B, Torres-Pérez R, Oliveros JC, Tsiantis M, Picó FX, Alonso-Blanco C. The trichome pattern diversity of Cardamine shares genetic mechanisms with Arabidopsis but differs in environmental drivers. Plant Physiol 2024:kiae213. [PMID: 38606947 DOI: 10.1093/plphys/kiae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Abstract
Natural variation in trichome pattern (amount and distribution) is prominent among populations of many angiosperms. However, the degree of parallelism in the genetic mechanisms underlying this diversity and its environmental drivers in different species remain unclear. To address these questions, we analyzed the genomic and environmental bases of leaf trichome pattern diversity in Cardamine hirsuta, a relative of Arabidopsis (Arabidopsis thaliana). We characterized 123 wild accessions for their genomic diversity, leaf trichome patterns at different temperatures, and environmental adjustments. Nucleotide diversities and biogeographical distribution models identified two major genetic lineages with distinct demographic and adaptive histories. Additionally, C. hirsuta showed substantial variation in trichome pattern and plasticity to temperature. Trichome amount in C. hirsuta correlated positively with spring precipitation but negatively with temperature, which is opposite to climatic patterns in A. thaliana. Contrastingly, genetic analysis of C. hirsuta glabrous accessions indicated that, like for A. thaliana, glabrousness is caused by null mutations in ChGLABRA1 (ChGL1). Phenotypic genome-wide association studies (GWAS) further identified a ChGL1 haplogroup associated with low trichome density and ChGL1 expression. Therefore, a ChGL1 series of null and partial loss-of-function alleles accounts for the parallel evolution of leaf trichome pattern in C. hirsuta and A. thaliana. Finally, GWAS also detected other candidate genes (e.g. ChETC3, ChCLE17) that might affect trichome pattern. Accordingly, the evolution of this trait in C. hirsuta and A. thaliana shows partially conserved genetic mechanisms but is likely involved in adaptation to different environments.
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Affiliation(s)
- Alberto Fuster-Pons
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Alba Murillo-Sánchez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Arnald Marcer
- CREAF, Cerdanyola del Vallès 08193, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Bjorn Pieper
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Francisco Xavier Picó
- Departamento de Biología evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
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Baumgarten L, Pieper B, Song B, Mane S, Lempe J, Lamb J, Cooke EL, Srivastava R, Strütt S, Žanko D, Casimiro PGP, Hallab A, Cartolano M, Tattersall AD, Huettel B, Filatov DA, Pavlidis P, Neuffer B, Bazakos C, Schaefer H, Mott R, Gan X, Alonso-Blanco C, Laurent S, Tsiantis M. Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns. PLoS Biol 2023; 21:e3002191. [PMID: 37463141 PMCID: PMC10353826 DOI: 10.1371/journal.pbio.3002191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/10/2023] [Indexed: 07/20/2023] Open
Abstract
We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.
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Affiliation(s)
- Lukas Baumgarten
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bjorn Pieper
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baoxing Song
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sébastien Mane
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Janne Lempe
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonathan Lamb
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Elizabeth L. Cooke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rachita Srivastava
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Stefan Strütt
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Danijela Žanko
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Asis Hallab
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maria Cartolano
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Crete, Greece
| | - Barbara Neuffer
- Department of Botany, University of Osnabrück, Osnabrück, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hanno Schaefer
- Department Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Richard Mott
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Wlodzimierz P, Rabanal FA, Burns R, Naish M, Primetis E, Scott A, Mandáková T, Gorringe N, Tock AJ, Holland D, Fritschi K, Habring A, Lanz C, Patel C, Schlegel T, Collenberg M, Mielke M, Nordborg M, Roux F, Shirsekar G, Alonso-Blanco C, Lysak MA, Novikova PY, Bousios A, Weigel D, Henderson IR. Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 2023:10.1038/s41586-023-06062-z. [PMID: 37198485 DOI: 10.1038/s41586-023-06062-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.
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Affiliation(s)
- Piotr Wlodzimierz
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Robin Burns
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Elias Primetis
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Nicola Gorringe
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Daniel Holland
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Katrin Fritschi
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Anette Habring
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christie Patel
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Theresa Schlegel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Miriam Mielke
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Vienna, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Polina Y Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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5
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Abbas M, Sharma G, Dambire C, Marquez J, Alonso-Blanco C, Proaño K, Holdsworth MJ. An oxygen-sensing mechanism for angiosperm adaptation to altitude. Nature 2022; 606:565-569. [PMID: 35650430 PMCID: PMC9200633 DOI: 10.1038/s41586-022-04740-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
Flowering plants (angiosperms) can grow at extreme altitudes, and have been observed growing as high as 6,400 metres above sea level1,2; however, the molecular mechanisms that enable plant adaptation specifically to altitude are unknown. One distinguishing feature of increasing altitude is a reduction in the partial pressure of oxygen (pO2). Here we investigated the relationship between altitude and oxygen sensing in relation to chlorophyll biosynthesis—which requires molecular oxygen3—and hypoxia-related gene expression. We show that in etiolated seedlings of angiosperm species, steady-state levels of the phototoxic chlorophyll precursor protochlorophyllide are influenced by sensing of atmospheric oxygen concentration. In Arabidopsis thaliana, this is mediated by the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway substrates GROUP VII ETHYLENE RESPONSE FACTOR transcription factors (ERFVIIs). ERFVIIs positively regulate expression of FLUORESCENT IN BLUE LIGHT (FLU), which represses the first committed step of chlorophyll biosynthesis, forming an inactivation complex with tetrapyrrole synthesis enzymes that are negatively regulated by ERFVIIs, thereby suppressing protochlorophyllide. In natural populations representing diverse angiosperm clades, we find oxygen-dependent altitudinal clines for steady-state levels of protochlorophyllide, expression of inactivation complex components and hypoxia-related genes. Finally, A. thaliana accessions from contrasting altitudes display altitude-dependent ERFVII activity and accumulation. We thus identify a mechanism for genetic adaptation to absolute altitude through alteration of the sensitivity of the oxygen-sensing system. Plants have adapted to grow at specific altitudes by regulating chlorophyll synthesis in response to ambient oxygen concentration, calibrated by altitude-dependent activity of GROUP VII ETHYLENE RESPONSE FACTOR.
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Affiliation(s)
- Mohamad Abbas
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Nottingham, UK
| | | | | | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Karina Proaño
- Laboratorio de Biotecnología Vegetal, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
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Arteaga N, Savic M, Méndez-Vigo B, Fuster-Pons A, Torres-Pérez R, Oliveros JC, Picó FX, Alonso-Blanco C. MYB transcription factors drive evolutionary innovations in Arabidopsis fruit trichome patterning. Plant Cell 2021; 33:548-565. [PMID: 33955486 PMCID: PMC8136876 DOI: 10.1093/plcell/koaa041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/24/2020] [Indexed: 05/27/2023]
Abstract
Both inter- and intra-specific diversity has been described for trichome patterning in fruits, which is presumably involved in plant adaptation. However, the mechanisms underlying this developmental trait have been hardly addressed. Here we examined natural populations of Arabidopsis (Arabidopsis thaliana) that develop trichomes in fruits and pedicels, phenotypes previously not reported in the Arabidopsis genus. Genetic analyses identified five loci, MALAMBRUNO 1-5 (MAU1-5), with MAU2, MAU3, and MAU5 showing strong epistatic interactions that are necessary and sufficient to display these traits. Functional characterization of these three loci revealed cis-regulatory mutations in TRICHOMELESS1 and TRIPTYCHON, as well as a structural mutation in GLABRA1. Therefore, the multiple mechanisms controlled by three MYB transcription factors of the core regulatory network for trichome patterning have jointly been modulated to trigger trichome development in fruits. Furthermore, analyses of worldwide accessions showed that these traits and mutations only occur in a highly differentiated relict lineage from the Iberian Peninsula. In addition, these traits and alleles were associated with low spring precipitation, which suggests that trichome development in fruits and pedicels might be involved in climatic adaptation. Thus, we show that the combination of synergistic mutations in a gene regulatory circuit has driven evolutionary innovations in fruit trichome patterning in Arabidopsis.
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Affiliation(s)
- Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Alberto Fuster-Pons
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
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Castilla AR, Méndez-Vigo B, Marcer A, Martínez-Minaya J, Conesa D, Picó FX, Alonso-Blanco C. Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evol Biol 2020; 20:71. [PMID: 32571210 PMCID: PMC7310121 DOI: 10.1186/s12862-020-01635-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation-isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)-in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. RESULTS IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana. In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana. CONCLUSIONS Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana.
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Affiliation(s)
- Antonio R Castilla
- Centre for Applied Ecology "Prof. Baeta Neves", InBIO, School of Agriculture, University of Lisbon, Lisbon, Portugal
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Centre de Recerca Ecològica i Aplicacions Forestals, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
| | | | - David Conesa
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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8
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Thiergart T, Durán P, Ellis T, Vannier N, Garrido-Oter R, Kemen E, Roux F, Alonso-Blanco C, Ågren J, Schulze-Lefert P, Hacquard S. Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nat Ecol Evol 2019; 4:122-131. [DOI: 10.1038/s41559-019-1063-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/08/2019] [Indexed: 11/09/2022]
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Delgado D, Sánchez-Bermejo E, de Marcos A, Martín-Jimenez C, Fenoll C, Alonso-Blanco C, Mena M. A Genetic Dissection of Natural Variation for Stomatal Abundance Traits in Arabidopsis. Front Plant Sci 2019; 10:1392. [PMID: 31781138 PMCID: PMC6859887 DOI: 10.3389/fpls.2019.01392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/09/2019] [Indexed: 05/20/2023]
Abstract
Stomatal abundance varies widely across natural populations of Arabidopsis thaliana, and presumably affects plant performance because it influences water and CO2 exchange with the atmosphere and thence photosynthesis and transpiration. In order to determine the genetic basis of this natural variation, we have analyzed a recombinant inbred line (RIL) population derived from the wild accession Ll-0 and the reference strain Landsberg erecta (Ler), which show low and high stomatal abundance, respectively. Quantitative trait locus (QTL) analyses of stomatal index, stomatal density, and pavement cell density measured in the adaxial cotyledon epidermis, identified five loci. Three of the genomic regions affect all traits and were named MID (Modulator of Cell Index and Density) 1 to 3. MID2 is a large-effect QTL overlapping with ERECTA (ER), the er-1 allele from Ler increasing all trait values. Additional analyses of natural and induced loss-of-function er mutations in different genetic backgrounds revealed that ER dysfunctions have differential and opposite effects on the stomatal index in adaxial and abaxial cotyledon epidermis and confirmed that ER is the gene underlying MID2. Ll-0 alleles at MID1 and MID3 displayed moderate and positive effects on the various traits. Furthermore, detailed developmental studies tracking primary and satellite stomatal lineages show that MID3-Ll-0 allele promotes the spacing divisions that initiate satellite lineages, while the ER allele limits them. Finally, expression analyses suggest that ER and MID3 modulate satellization through partly different regulatory pathways. Our characterization of MID3 indicates that genetic modulation of satellization contributes to the variation for stomatal abundance in natural populations, and subsequently that this trait might be involved in plant adaptation.
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Affiliation(s)
- Dolores Delgado
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Eduardo Sánchez-Bermejo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alberto de Marcos
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Cristina Martín-Jimenez
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carmen Fenoll
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Montaña Mena
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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10
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Méndez-Vigo B, Ausín I, Zhu W, Mollá-Morales A, Balasubramanian S, Alonso-Blanco C. Genetic Interactions and Molecular Evolution of the Duplicated Genes ICARUS2 and ICARUS1 Help Arabidopsis Plants Adapt to Different Ambient Temperatures. Plant Cell 2019; 31:1222-1237. [PMID: 30992321 PMCID: PMC6588312 DOI: 10.1105/tpc.18.00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/29/2019] [Accepted: 04/12/2019] [Indexed: 05/30/2023]
Abstract
Understanding how plants adapt to ambient temperatures has become a major challenge prompted by global climate change. This has led to the identification of several genes regulating the thermal plasticity of plant growth and flowering time. However, the mechanisms accounting for the natural variation and evolution of such developmental plasticity remain mostly unknown. In this study, we determined that natural variation at ICARUS2 (ICA2), which interacts genetically with its homolog ICA1, alters growth and flowering time plasticity in relation to temperature in Arabidopsis (Arabidopsis thaliana). Transgenic analyses demonstrated multiple functional effects for ICA2 and supported the notion that structural polymorphisms in ICA2 likely underlie its natural variation. Two major ICA2 haplogroups carrying distinct functionally active alleles showed high frequency, strong geographic structure, and significant associations with climatic variables related to annual and daily fluctuations in temperature. Genome analyses across the plant phylogeny indicated that the prevalent plant ICA genes encoding two tRNAHis guanylyl transferase 1 units evolved ∼120 million years ago during the early divergence of mono- and dicotyledonous clades. In addition, ICA1/ICA2 duplication occurred specifically in the Camelineae tribe (Brassicaceae). Thus, ICA2 appears to be ubiquitous across plant evolution and likely contributes to climate adaptation through modifications of thermal developmental plasticity in Arabidopsis.
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Affiliation(s)
- Belén Méndez-Vigo
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Israel Ausín
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wangsheng Zhu
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Almudena Mollá-Morales
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | | | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
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11
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Montes N, Alonso-Blanco C, García-Arenal F. Cucumber mosaic virus infection as a potential selective pressure on Arabidopsis thaliana populations. PLoS Pathog 2019; 15:e1007810. [PMID: 31136630 PMCID: PMC6555541 DOI: 10.1371/journal.ppat.1007810] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/07/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023] Open
Abstract
It has been proposed that in wild ecosystems viruses are often plant mutualists, whereas agroecosystems favour pathogenicity. We seek evidence for virus pathogenicity in wild ecosystems through the analysis of plant-virus coevolution, which requires a negative effect of infection on the host fitness. We focus on the interaction between Arabidopsis thaliana and Cucumber mosaic virus (CMV), which is significant in nature. We studied the genetic diversity of A. thaliana for two defence traits, resistance and tolerance, to CMV. A set of 185 individuals collected in 76 A. thaliana Iberian wild populations were inoculated with different CMV strains. Resistance was estimated from the level of virus multiplication in infected plants, and tolerance from the effect of infection on host progeny production. Resistance and tolerance to CMV showed substantial genetic variation within and between host populations, and depended on the virus x host genotype interaction, two conditions for coevolution. Resistance and tolerance were co-occurring independent traits that have evolved independently from related life-history traits involved in adaptation to climate. The comparison of the genetic structure for resistance and tolerance with that for neutral traits (QST/FST analyses) indicated that both defence traits are likely under uniform selection. These results strongly suggest that CMV infection selects for defence on A. thaliana populations, and support plant-virus coevolution. Thus, we propose that CMV infection reduces host fitness under the field conditions of the wild A. thaliana populations studied.
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Affiliation(s)
- Nuria Montes
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus Universidad Autónoma, Cantoblanco, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), Spain
- * E-mail:
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12
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Martínez-Minaya J, Conesa D, Fortin MJ, Alonso-Blanco C, Picó FX, Marcer A. A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts. Mol Ecol Resour 2019; 19:929-943. [PMID: 30993910 DOI: 10.1111/1755-0998.13024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022]
Abstract
Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Both factors reflect the joint effect of ecoevolutionary processes on the geographical heterogeneity of populations. We used a collection of 301 georeferenced accessions of the annual plant Arabidopsis thaliana in its Iberian Peninsula range, where the species shows strong geographical genetic structure. We developed spatial and nonspatial hierarchical Bayesian models (HBMs) to depict current and future distribution ranges for the four genetic clusters detected. We also compared the performance of HBMs with Maxent (a presence-only model). Maxent and nonspatial HBMs presented some shortcomings, such as the loss of accessions with high genetic admixture in the case of Maxent and the presence of residual SAC for both. As spatial HBMs removed residual SAC, these models showed higher accuracy than nonspatial HBMs and handled the spatial effect on model outcomes. The ease of modelling and the consistency among model outputs for each genetic cluster was conditioned by the sparseness of the populations across the distribution range. Our HBMs enrich the toolbox of software available to evaluate GCC-induced distribution range shifts by considering both genetic heterogeneity and SAC, two inherent properties of any organism that should not be overlooked.
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Affiliation(s)
- Joaquín Martínez-Minaya
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - David Conesa
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Arnald Marcer
- CREAF, Bellaterra (Cerdanyola del Vallès), Spain.,Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
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13
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Gómez R, Méndez-Vigo B, Marcer A, Alonso-Blanco C, Picó FX. Quantifying temporal change in plant population attributes: insights from a resurrection approach. AoB Plants 2018; 10:ply063. [PMID: 30370042 PMCID: PMC6198925 DOI: 10.1093/aobpla/ply063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/05/2018] [Indexed: 05/11/2023]
Abstract
Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to rapid environmental shifts, such as the ones imposed by global climate change. To that end, we undertook a resurrection approach in Spanish populations of the annual plant Arabidopsis thaliana that were sampled twice over a decade. Annual weather records were compared to their historical records to extract patterns of climatic shifts over time. We evaluated the differences between samplings in flowering time, a key life-history trait with adaptive significance, with a field experiment. We also estimated genetic diversity and differentiation based on neutral nuclear markers and nucleotide diversity in candidate flowering time (FRI and FLC) and seed dormancy (DOG1) genes. The role of genetic drift was estimated by computing effective population sizes with the temporal method. Overall, two climatic scenarios were detected: intense warming with increased precipitation and moderate warming with decreased precipitation. The average flowering time varied little between samplings. Instead, within-population variation in flowering time exhibited a decreasing trend over time. Substantial temporal changes in genetic diversity and differentiation were observed with both nuclear microsatellites and candidate genes in all populations, which were interpreted as the result of natural demographic fluctuations. We conclude that drought stress caused by moderate warming with decreased precipitation may have the potential to reduce within-population variation in key life-cycle traits, perhaps as a result of stabilizing selection on them, and to constrain the genetic differentiation over time. Besides, the demographic behaviour of populations probably accounts for the substantial temporal patterns of genetic variation, while keeping rather constant those of phenotypic variation.
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Affiliation(s)
- Rocío Gómez
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Corresponding author’s e-mail address:
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14
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Tabas-Madrid D, Méndez-Vigo B, Arteaga N, Marcer A, Pascual-Montano A, Weigel D, Xavier Picó F, Alonso-Blanco C. Genome-wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana. Plant Cell Environ 2018; 41:1806-1820. [PMID: 29520809 DOI: 10.1111/pce.13189] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 05/25/2023]
Abstract
Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome-wide associations identified known (Twin Sister of FT, FRIGIDA-like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage-Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.
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Affiliation(s)
- Daniel Tabas-Madrid
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Arnald Marcer
- CREAF, 08193, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Alberto Pascual-Montano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
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15
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Parás-Bravo P, Paz-Zulueta M, Alonso-Blanco C, Salvadores-Fuentes P, Ruiz-Azcona L, Santibañez M. Presence of cancer pain, inadequate pain control and psychotropic drug use: A cross-selectional study. Rev Epidemiol Sante Publique 2018. [DOI: 10.1016/j.respe.2018.05.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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16
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Exposito-Alonso M, Brennan AC, Alonso-Blanco C, Picó FX. Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana. Evolution 2018; 72:1570-1586. [PMID: 29947421 DOI: 10.1111/evo.13508] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 12/31/2022]
Abstract
The evolutionary response of organisms to global climate change is expected to be strongly conditioned by preexisting standing genetic variation. In addition, natural selection imposed by global climate change on fitness-related traits can be heterogeneous over time. We estimated selection of life-history traits of an entire genetic lineage of the plant Arabidopsis thaliana occurring in north-western Iberian Peninsula that were transplanted over multiple years into two environmentally contrasting field sites in southern Spain, as southern environments are expected to move progressively northwards with climate change in the Iberian Peninsula. The results indicated that natural selection on flowering time prevailed over that on recruitment. Selection favored early flowering in six of eight experiments and late flowering in the other two. Such heterogeneity of selection for flowering time might be a powerful mechanism for maintaining genetic diversity in the long run. We also found that north-western A. thaliana accessions from warmer environments exhibited higher fitness and higher phenotypic plasticity for flowering time in southern experimental facilities. Overall, our transplant experiments suggested that north-western Iberian A. thaliana has the means to cope with increasingly warmer environments in the region as predicted by trends in global climate change models.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, United Kingdom
| | - 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 Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
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17
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Marcer A, Vidigal DS, James PMA, Fortin MJ, Méndez-Vigo B, Hilhorst HWM, Bentsink L, Alonso-Blanco C, Picó FX. Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically. Plant Biol (Stuttg) 2018; 20 Suppl 1:148-156. [PMID: 28241389 DOI: 10.1111/plb.12558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
To understand how adaptive evolution in life-cycle phenology operates in plants, we need to unravel the effects of geographic variation in putative agents of natural selection on life-cycle phenology by considering all key developmental transitions and their co-variation patterns. We address this goal by quantifying the temperature-driven and geographically varying relationship between seed dormancy and flowering time in the annual Arabidopsis thaliana across the Iberian Peninsula. We used data on genetic variation in two major life-cycle traits, seed dormancy (DSDS50) and flowering time (FT), in a collection of 300 A. thaliana accessions from the Iberian Peninsula. The geographically varying relationship between life-cycle traits and minimum temperature, a major driver of variation in DSDS50 and FT, was explored with geographically weighted regressions (GWR). The environmentally varying correlation between DSDS50 and FT was analysed by means of sliding window analysis across a minimum temperature gradient. Maximum local adjustments between minimum temperature and life-cycle traits were obtained in the southwest Iberian Peninsula, an area with the highest minimum temperatures. In contrast, in off-southwest locations, the effects of minimum temperature on DSDS50 were rather constant across the region, whereas those of minimum temperature on FT were more variable, with peaks of strong local adjustments of GWR models in central and northwest Spain. Sliding window analysis identified a minimum temperature turning point in the relationship between DSDS50 and FT around a minimum temperature of 7.2 °C. Above this minimum temperature turning point, the variation in the FT/DSDS50 ratio became rapidly constrained and the negative correlation between FT and DSDS50 did not increase any further with increasing minimum temperatures. The southwest Iberian Peninsula emerges as an area where variation in life-cycle phenology appears to be restricted by the duration and severity of the hot summer drought. The temperature-driven varying relationship between DSDS50 and FT detected environmental boundaries for the co-evolution between FT and DSDS50 in A. thaliana. In the context of global warming, we conclude that A. thaliana phenology from the southwest Iberian Peninsula, determined by early flowering and deep seed dormancy, might become the most common life-cycle phenotype for this annual plant in the region.
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Affiliation(s)
- A Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Univ. Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - D S Vidigal
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - P M A James
- Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
| | - M-J Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - B Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - H W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - L Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - C Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F X Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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18
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Fernández-de-Las-Peñas C, Cleland J, Palacios-Ceña M, Fuensalida-Novo S, Alonso-Blanco C, Pareja JA, Alburquerque-Sendín F. Effectiveness of manual therapy versus surgery in pain processing due to carpal tunnel syndrome: A randomized clinical trial. Eur J Pain 2017; 21:1266-1276. [PMID: 28295825 DOI: 10.1002/ejp.1026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND People with carpal tunnel syndrome (CTS) exhibit widespread pressure pain and thermal pain hypersensitivity as a manifestation of central sensitization. The aim of our study was to compare the effectiveness of manual therapy versus surgery for improving pain and nociceptive gain processing in people with CTS. METHODS The trial was conducted at a local regional Hospital in Madrid, Spain from August 2014 to February 2015. In this randomized parallel-group, blinded, clinical trial, 100 women with CTS were randomly allocated to either manual therapy (n = 50), who received three sessions (once/week) of manual therapies including desensitization manoeuvres of the central nervous system, or surgical intervention (n = 50) group. Outcomes including pressure pain thresholds (PPT), thermal pain thresholds (HPT or CPT), and pain intensity which were assessed at baseline, and 3, 6, 9 and 12 months after the intervention by an assessor unaware of group assignment. Analysis was by intention to treat with mixed ANCOVAs adjusted for baseline scores. RESULTS At 12 months, 95 women completed the follow-up. Patients receiving manual therapy exhibited higher increases in PPT over the carpal tunnel at 3, 6 and 9 months (all, p < 0.01) and higher decrease of pain intensity at 3 month follow-up (p < 0.001) than those receiving surgery. No significant differences were observed between groups for the remaining outcomes. CONCLUSIONS Manual therapy and surgery have similar effects on decreasing widespread pressure pain sensitivity and pain intensity in women with CTS. Neither manual therapy nor surgery resulted in changes in thermal pain sensitivity. SIGNIFICANCE The current study found that manual therapy and surgery exhibited similar effects on decreasing widespread pressure pain sensitivity and pain intensity in women with carpal tunnel syndrome at medium- and long-term follow-ups investigating changes in nociceptive gain processing after treatment in carpal tunnel syndrome.
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Affiliation(s)
- C Fernández-de-Las-Peñas
- Department of Physical Therapy, Occupational Therapy, Rehabilitation and Physical Medicine, Universidad Rey Juan Carlos, Alcorcón, Spain
| | - J Cleland
- Department of Physical Therapy, Franklin Pierce University, Manchester, USA.,Rehabilitation Services, Concord Hospital, USA.,Manual Therapy Fellowship Program, Regis University, Denver, USA
| | - M Palacios-Ceña
- Department of Physical Therapy, Occupational Therapy, Rehabilitation and Physical Medicine, Universidad Rey Juan Carlos, Alcorcón, Spain
| | - S Fuensalida-Novo
- Department of Physical Therapy, Occupational Therapy, Rehabilitation and Physical Medicine, Universidad Rey Juan Carlos, Alcorcón, Spain
| | - C Alonso-Blanco
- Department of Physical Therapy, Occupational Therapy, Rehabilitation and Physical Medicine, Universidad Rey Juan Carlos, Alcorcón, Spain
| | - J A Pareja
- Department of Neurology and Neurophysiology, Hospital Universitario Fundación Alcorcón, Madrid, Spain
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19
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Lee CR, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova P, Alonso-Blanco C, Weigel D, Nordborg M. On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun 2017; 8:14458. [PMID: 28181519 PMCID: PMC5309843 DOI: 10.1038/ncomms14458] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/03/2017] [Indexed: 02/03/2023] Open
Abstract
Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these 'relicts' occupied post-glacial Eurasia first and were later replaced by the invading 'non-relicts', which expanded through the east-west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats.
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Affiliation(s)
- Cheng-Ruei Lee
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, 10617 Taipei, Taiwan
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Moises Exposito-Alonso
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Wei Ding
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Polina Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
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20
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Vidigal DS, Marques ACSS, Willems LAJ, Buijs G, Méndez-Vigo B, Hilhorst HWM, Bentsink L, Picó FX, Alonso-Blanco C. Altitudinal and climatic associations of seed dormancy and flowering traits evidence adaptation of annual life cycle timing in Arabidopsis thaliana. Plant Cell Environ 2016; 39:1737-1748. [PMID: 26991665 DOI: 10.1111/pce.12734] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
The temporal control or timing of the life cycle of annual plants is presumed to provide adaptive strategies to escape harsh environments for survival and reproduction. This is mainly determined by the timing of germination, which is controlled by the level of seed dormancy, and of flowering initiation. However, the environmental factors driving the evolution of plant life cycles remain largely unknown. To address this question we have analysed nine quantitative life history traits, in a native regional collection of 300 wild accessions of Arabidopsis thaliana. Seed dormancy and flowering time were negatively correlated, indicating that these traits have coevolved. In addition, environmental-phenotypic analyses detected strong altitudinal and climatic clines for most life history traits. Overall, accessions showing life cycles with early flowering, small seeds, high seed dormancy and slow germination rate were associated with locations exposed to high temperature, low summer precipitation and high radiation. Furthermore, we analysed the expression level of the positive regulator of seed dormancy DELAY OF GERMINATION 1 (DOG1), finding similar but weaker altitudinal and climatic patterns than seed dormancy. Therefore, DOG1 regulatory mutations are likely to provide a quantitative molecular mechanism for the adaptation of A. thaliana life cycle to altitude and climate.
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Affiliation(s)
- Deborah S Vidigal
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Alexandre C S S Marques
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Gonda Buijs
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Leónie Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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21
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Fernández-de-las-Peñas C, Alonso-Blanco C, Cuadrado ML, Pareja JA. Neck Mobility and Forward Head Posture are not Related to Headache Parameters in Chronic Tension-Type Headache. Cephalalgia 2016; 27:158-64. [PMID: 17257237 DOI: 10.1111/j.1468-2982.2006.01247.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The relationship between the changes in forward head posture (FHP), neck mobility and headache parameters was analysed in 25 patients with chronic tension-type headache (CTTH) undergoing a physical therapy programme. Side-view pictures were taken to measure the cranio-vertebral angle in the sitting and standing positions. A cervical goniometer was employed to measure the range of all cervical motions. A headache diary was kept to assess headache intensity, frequency and duration. All patients received six sessions of physical therapy over 3 weeks. Outcomes were assessed at baseline, after treatment and 1 month later. Neck mobility and headache parameters showed a significant improvement after the intervention, whereas posture changes did not reach statistical significance. No correlations were found between FHP, neck mobility and headache parameters at any stage. Changes in these outcomes throughout the study were not correlated either. FHP and neck mobility appear not to be related to headache intensity, duration or frequency in patients suffering from CTTH. Although patients showed a reduction in the range of motion in the neck, it is uncertain whether this is consistent with TTH.
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Affiliation(s)
- C Fernández-de-las-Peñas
- Department of Physical Therapy, Occupational Therapy, Physical Medicine and Rehabilitation, Universidad Rey Juan Carlos, Madrid, Spain.
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22
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Marcer A, Méndez-Vigo B, Alonso-Blanco C, Picó FX. Tackling intraspecific genetic structure in distribution models better reflects species geographical range. Ecol Evol 2016; 6:2084-97. [PMID: 27066224 PMCID: PMC4768750 DOI: 10.1002/ece3.2010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 12/25/2022] Open
Abstract
Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.
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Affiliation(s)
- Arnald Marcer
- CREAF Cerdanyola del Vallès 08193 Spain; Univ Autònoma de Barcelona Cerdanyola del Vallès 08193 Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas Centro Nacional de Biotecnología (CNB) Consejo Superior de Investigaciones Científicas (CSIC) 28049 Madrid Spain
| | - 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 Ecología Integrativa Estación Biológica de Doñana (EBD) Consejo Superior de Investigaciones Científicas (CSIC) 41092 Sevilla Spain
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23
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. Plant Cell Environ 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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24
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Abe M, Kaya H, Watanabe-Taneda A, Shibuta M, Yamaguchi A, Sakamoto T, Kurata T, Ausín I, Araki T, Alonso-Blanco C. FE, a phloem-specific Myb-related protein, promotes flowering through transcriptional activation of FLOWERING LOCUS T and FLOWERING LOCUS T INTERACTING PROTEIN 1. Plant J 2015; 83:1059-68. [PMID: 26239308 DOI: 10.1111/tpj.12951] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/24/2015] [Accepted: 07/17/2015] [Indexed: 05/21/2023]
Abstract
In many flowering plants, the transition to flowering is primarily affected by seasonal changes in day length (photoperiod). An inductive photoperiod promotes flowering via synthesis of a floral stimulus, called florigen. In Arabidopsis thaliana, the FLOWERING LOCUS T (FT) protein is an essential component of florigen, which is synthesized in leaf phloem companion cells and is transported through phloem tissue to the shoot apical meristem where floral morphogenesis is initiated. However, the molecular mechanism involved in the long-distance transport of FT protein remains elusive. In this study, we characterized the classic Arabidopsis mutant fe, which is involved in the photoperiodic induction of flowering, and showed that FE encodes a phloem-specific Myb-related protein that was previously reported as ALTERED PHLOEM DEVELOPMENT. Phenotypic analyses of the fe mutant showed that FT expression is reduced in leaf phloem companion cells. In addition, the transport of FT protein from leaves to the shoot apex is impaired in the fe mutant. Expression analyses further demonstrated that FE is also required for transcriptional activation of FLOWERING LOCUS T INTERACTING PROTEIN 1 (FTIP1), an essential regulator for selective trafficking of the FT protein from companion cells to sieve elements. These findings indicate that FE plays a dual role in the photoperiodic induction of flowering: as a transcriptional activator of FT on the one hand, and its transport machinery component, FTIP1, on the other hand. Thus, FE is likely to play a role in regulating FT by coordinating FT synthesis and FT transport in phloem companion cells.
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Affiliation(s)
- Mitsutomo Abe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hidetaka Kaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ayako Watanabe-Taneda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mio Shibuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ayako Yamaguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Graduate School of Biostudies, Kyoto University, Yoshida Konoecho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Yoshida Konoecho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
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25
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Zhu W, Ausin I, Seleznev A, Méndez-Vigo B, Picó FX, Sureshkumar S, Sundaramoorthi V, Bulach D, Powell D, Seemann T, Alonso-Blanco C, Balasubramanian S. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005085. [PMID: 25951176 PMCID: PMC4423873 DOI: 10.1371/journal.pgen.1005085] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/20/2015] [Indexed: 12/17/2022] Open
Abstract
Plants are highly sensitive to environmental changes and even small variations in ambient temperature have severe consequences on their growth and development. Temperature affects multiple aspects of plant development, but the processes and mechanisms underlying thermo-sensitive growth responses are mostly unknown. Here we exploit natural variation in Arabidopsis thaliana to identify and characterize novel components and processes mediating thermo-sensitive growth responses in plants. Phenotypic screening of wild accessions identified several strains displaying pleiotropic growth defects, at cellular and organism levels, specifically at high ambient temperatures. Positional cloning and characterization of the underlying gene revealed that ICARUS1 (ICA1), which encodes a protein of the tRNAHis guanylyl transferase (Thg1) superfamily, is required for plant growth at high temperatures. Transcriptome and gene marker analyses together with DNA content measurements show that ICA1 loss-of-function results in down regulation of cell cycle associated genes at high temperatures, which is linked with a block in G2/M transition and endoreduplication. In addition, plants with mutations in ICA1 show enhanced sensitivity to DNA damage. Characterization of additional strains that carry lesions in ICA1, but display normal growth, shows that alternative splicing is likely to alleviate the deleterious effects of some natural mutations. Furthermore, analyses of worldwide and regional collections of natural accessions indicate that ICA1 loss-of-function has arisen several times independently, and that these occur at high frequency in some local populations. Overall our results suggest that ICA1-mediated-modulation of fundamental processes such as tRNAHis maturation, modify plant growth responses to temperature changes in a quantitative and reversible manner, in natural populations. The increase in average temperatures across the globe has been predicted to have negative impacts on agricultural productivity. Therefore, there is a need to understand the molecular mechanisms that underlie plant growth responses to varying temperature regimes. At present, very little is known about the genes and pathways that modulate thermo-sensory growth responses in plants. In this article, the authors exploit natural variation in the commonly occurring weed thale cress (Arabidopsis thaliana) and identify a gene referred to as ICARUS1 to be required for plant growth at higher ambient temperatures. Plants carrying lesions in this gene stop growing at high temperatures and revert to growth when temperatures reduce. Using a combination of computational, molecular and cell biological approaches, the authors demonstrate that allelic variation at ICARUS1, which encodes an enzyme required for the fundamental biochemical process of tRNAHis maturation, underlies variation in thermo-sensory growth responses of A. thaliana. Furthermore, the authors discover that the deleterious impact of a natural mutation in ICARUS1 is suppressed through alternative splicing, thus suggesting the potential for alternative splicing to buffer the impacts of some natural mutations. These results support that modulation of fundamental processes, in addition to transcriptional regulation, mediate thermo-sensory growth responses in plants.
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Affiliation(s)
- Wangsheng Zhu
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Israel Ausin
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F. Xavier Picó
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | | | | | - Dieter Bulach
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - David Powell
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (CAB); (SB)
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26
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Willing EM, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJV, Becker C, Warthmann N, Chica C, Szarzynska B, Zytnicki M, Albani MC, Kiefer C, Bergonzi S, Castaings L, Mateos JL, Berns MC, Bujdoso N, Piofczyk T, de Lorenzo L, Barrero-Sicilia C, Mateos I, Piednoël M, Hagmann J, Chen-Min-Tao R, Iglesias-Fernández R, Schuster SC, Alonso-Blanco C, Roudier F, Carbonero P, Paz-Ares J, Davis SJ, Pecinka A, Quesneville H, Colot V, Lysak MA, Weigel D, Coupland G, Schneeberger K. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants 2015; 1:14023. [PMID: 27246759 DOI: 10.1038/nplants.2014.23] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/10/2014] [Indexed: 05/10/2023]
Abstract
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
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Affiliation(s)
- Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Terezie Mandáková
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Karl J V Nordström
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Claudia Chica
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Bogna Szarzynska
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Matthias Zytnicki
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Maria C Albani
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Sara Bergonzi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Loren Castaings
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Julieta L Mateos
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Markus C Berns
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Nora Bujdoso
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Thomas Piofczyk
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Laura de Lorenzo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Barrero-Sicilia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Isabel Mateos
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Romy Chen-Min-Tao
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Stephan C Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Martin A Lysak
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
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Alonso-Blanco C, Méndez-Vigo B. Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis. Curr Opin Plant Biol 2014; 18:37-43. [PMID: 24565952 DOI: 10.1016/j.pbi.2014.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 05/08/2023]
Abstract
Deciphering the genetic and molecular bases of quantitative variation is a long-standing challenge in plant biology because it is essential for understanding evolution and for accelerating plant breeding. Recent multi-trait analyses at different phenotypic levels are uncovering the pleiotropy and the genetic regulation underlying high-level complex traits. Thus, the number of known causal loci, genes and nucleotide polymorphisms is expanding. Current plant causal catalogs contain ∼400 genes and natural polymorphisms revealing several dysfunctional allelic series that involve multiple mutations. In addition, repeated evolution of quantitative traits mediated by large effect alleles is found across plant phylogeny. Finally, systematic analyses of genetic and environmental interactions are beginning to elucidate the molecular mechanisms of relevant interactions.
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Affiliation(s)
- Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain.
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain
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Manzano-Piedras E, Marcer A, Alonso-Blanco C, Picó FX. Deciphering the adjustment between environment and life history in annuals: lessons from a geographically-explicit approach in Arabidopsis thaliana. PLoS One 2014; 9:e87836. [PMID: 24498381 PMCID: PMC3912251 DOI: 10.1371/journal.pone.0087836] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022] Open
Abstract
The role that different life-history traits may have in the process of adaptation caused by divergent selection can be assessed by using extensive collections of geographically-explicit populations. This is because adaptive phenotypic variation shifts gradually across space as a result of the geographic patterns of variation in environmental selective pressures. Hence, large-scale experiments are needed to identify relevant adaptive life-history traits as well as their relationships with putative selective agents. We conducted a field experiment with 279 geo-referenced accessions of the annual plant Arabidopsis thaliana collected across a native region of its distribution range, the Iberian Peninsula. We quantified variation in life-history traits throughout the entire life cycle. We built a geographic information system to generate an environmental data set encompassing climate, vegetation and soil data. We analysed the spatial autocorrelation patterns of environmental variables and life-history traits, as well as the relationship between environmental and phenotypic data. Almost all environmental variables were significantly spatially autocorrelated. By contrast, only two life-history traits, seed weight and flowering time, exhibited significant spatial autocorrelation. Flowering time, and to a lower extent seed weight, were the life-history traits with the highest significant correlation coefficients with environmental factors, in particular with annual mean temperature. In general, individual fitness was higher for accessions with more vigorous seed germination, higher recruitment and later flowering times. Variation in flowering time mediated by temperature appears to be the main life-history trait by which A. thaliana adjusts its life history to the varying Iberian environmental conditions. The use of extensive geographically-explicit data sets obtained from field experiments represents a powerful approach to unravel adaptive patterns of variation. In a context of current global warming, geographically-explicit approaches, evaluating the match between organisms and the environments where they live, may contribute to better assess and predict the consequences of global warming.
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Affiliation(s)
- Esperanza Manzano-Piedras
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Arnald Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F. Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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Brennan AC, Méndez-Vigo B, Haddioui A, Martínez-Zapater JM, Picó FX, Alonso-Blanco C. The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe. BMC Plant Biol 2014; 14:17. [PMID: 24411008 PMCID: PMC3890648 DOI: 10.1186/1471-2229-14-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown. RESULTS To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia. CONCLUSIONS The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia.
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Affiliation(s)
- Adrian C Brennan
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Abdelmajid Haddioui
- Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | - José M Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - F Xavier Picó
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Méndez-Vigo B, Gomaa NH, Alonso-Blanco C, Xavier Picó F. Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. New Phytol 2013; 197:1332-1343. [PMID: 23252608 DOI: 10.1111/nph.12082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/05/2012] [Indexed: 05/08/2023]
Abstract
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct Q(ST)-F(ST) comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Nasr H Gomaa
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - 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 Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
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Méndez-Vigo B, Martínez-Zapater JM, Alonso-Blanco C. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background. PLoS Genet 2013; 9:e1003289. [PMID: 23382706 PMCID: PMC3561112 DOI: 10.1371/journal.pgen.1003289] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/15/2012] [Indexed: 01/17/2023] Open
Abstract
The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time. In many plant species, the timing of flowering initiation shows abundant quantitative variation among natural varieties, which reflects the importance of this trait for adaptation to different environments. Currently, a major goal in plant biology is to determine the molecular and evolutionary bases of this natural genetic variation. In this study we demonstrate that the central flowering regulator SHORT VEGETATIVE PHASE (SVP), encoding a MADS transcription factor, is involved in the flowering natural variation of the model organism Arabidopsis thaliana. In particular, we prove that a structural change caused by a single amino acid substitution generates a SVP early flowering allele that is distributed only in Asia. Furthermore, genetic interactions have been shown to be a component of the natural variation for many important adaptive traits. However, very few studies, either in animals or plants, have systematically addressed the extent of genetic interactions among specific alleles responsible for the natural variation of complex traits. Our study shows that the flowering effects of SVP natural alleles depend significantly on the genetic background; and, subsequently, we demonstrate the relevance of epistasis for the evolution of this crucial transcription factor and flowering time.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José M. Martínez-Zapater
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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Sánchez-Bermejo E, Méndez-Vigo B, Picó FX, Martínez-Zapater JM, Alonso-Blanco C. Novel natural alleles at FLC and LVR loci account for enhanced vernalization responses in Arabidopsis thaliana. Plant Cell Environ 2012; 35:1672-84. [PMID: 22494398 DOI: 10.1111/j.1365-3040.2012.02518.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Vernalization, the induction of flowering by low winter temperatures, is likely to be involved in plant climatic adaptation. However, the genetic, molecular and ecological bases underlying the quantitative variation that tunes vernalization sensitivity to natural environments are largely unknown. To address these questions, we have studied the enhanced vernalization response shown by the Ll-0 accession of Arabidopsis thaliana. Quantitative trait locus (QTL) mapping for several flowering initiation traits in relation to vernalization, in a new Ler × Ll-0 recombinant inbred line (RIL) population, identified large effect alleles at FRI, FLC and HUA2, together with two small effect loci named as Llagostera vernalization response (LVR) 1 and 2. Phenotypic analyses of near isogenic lines validated LVR1 effect on flowering vernalization responses. To further characterize the FLC allele from Ll-0, we carried out genetic association analyses using a regional collection of wild genotypes. FLC-Ll-0 appeared as a low-frequency allele that is distinguished by polymorphism Del(-57), a 50-bp-deletion in the 5'-UTR. Del(-57) was significantly associated with enhanced vernalization responses and FLC RNA expression, as well as with altitude and minimum temperatures. These results are consistent with Del(-57) acting as a novel cis-regulatory FLC polymorphism that may confer climatic adaptation by increasing vernalization sensitivity.
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Affiliation(s)
- Eduardo Sánchez-Bermejo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
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Kronholm I, Picó FX, Alonso-Blanco C, Goudet J, de Meaux J. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. Evolution 2012. [PMID: 22759302 DOI: 10.5061/dryad.4rp76r87] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.
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Affiliation(s)
- Ilkka Kronholm
- Department Genetics and Plant Breeding, Max Planck Institute for Plant Breeding Research, DE-50829 Cologne, Germany
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Kronholm I, Picó FX, Alonso-Blanco C, Goudet J, de Meaux J. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. Evolution 2012; 66:2287-302. [PMID: 22759302 DOI: 10.1111/j.1558-5646.2012.01590.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.
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Affiliation(s)
- Ilkka Kronholm
- Department Genetics and Plant Breeding, Max Planck Institute for Plant Breeding Research, DE-50829 Cologne, Germany
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35
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Méndez-Vigo B, Picó FX, Ramiro M, Martínez-Zapater JM, Alonso-Blanco C. Altitudinal and climatic adaptation is mediated by flowering traits and FRI, FLC, and PHYC genes in Arabidopsis. Plant Physiol 2011; 157:1942-55. [PMID: 21988878 PMCID: PMC3327218 DOI: 10.1104/pp.111.183426] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/10/2011] [Indexed: 05/19/2023]
Abstract
Extensive natural variation has been described for the timing of flowering initiation in many annual plants, including the model wild species Arabidopsis (Arabidopsis thaliana), which is presumed to be involved in adaptation to different climates. However, the environmental factors that might shape this genetic variation, as well as the molecular bases of climatic adaptation by modifications of flowering time, remain mostly unknown. To approach both goals, we characterized the flowering behavior in relation to vernalization of 182 Arabidopsis wild genotypes collected in a native region spanning a broad climatic range. Phenotype-environment association analyses identified strong altitudinal clines (0-2600 m) in seven out of nine flowering-related traits. Altitudinal clines were dissected in terms of minimum winter temperature and precipitation, indicating that these are the main climatic factors that might act as selective pressures on flowering traits. In addition, we used an association analysis approach with four candidate genes, FRIGIDA (FRI), FLOWERING LOCUS C (FLC), PHYTOCHROME C (PHYC), and CRYPTOCHROME2, to decipher the genetic bases of this variation. Eleven different loss-of-function FRI alleles of low frequency accounted for up to 16% of the variation for most traits. Furthermore, an FLC allelic series of six novel putative loss- and change-of-function alleles, with low to moderate frequency, revealed that a broader FLC functional diversification might contribute to flowering variation. Finally, environment-genotype association analyses showed that the spatial patterns of FRI, FLC, and PHYC polymorphisms are significantly associated with winter temperatures and spring and winter precipitations, respectively. These results support that allelic variation in these genes is involved in climatic adaptation.
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Affiliation(s)
| | | | | | | | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain (B.M.-V., M.R., J.M.M.-Z., C.A.-B.); Departamento de Ecología Integrativa, Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Seville 41092, Spain (F.X.P.); Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja, Logrono 26006, Spain (J.M.M.-Z.)
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Fernández-de-las-Peñas C, Alonso-Blanco C, Miangolarra JC. Myofascial trigger points in subjects presenting with mechanical neck pain: a blinded, controlled study. ACTA ACUST UNITED AC 2011; 12:29-33. [PMID: 21882489 DOI: 10.1016/j.math.2006.02.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The aim of this study was to describe the differences in the presence of myofascial trigger points (TrPs) in the upper trapezius,sternocleidomastoid, levator scapulae and suboccipital muscles between patients presenting with mechanical neck pain and control healthy subjects. Twenty subjects with mechanical neck pain and 20 matched healthy controls participated in this study. TrPs were identified, by an assessor blinded to the subjects' condition, when there was a hypersensible tender spot in a palpable taut band, local twitch response elicited by the snapping palpation of the taut band, and reproduction of the referred pain typical of each TrP. The mean number of TrPs present on each neck pain patient was 4.3 (SD: 0.9), of which 2.5 (SD: 1.3) were latent and 1.8 (SD: 0.8) were active TrPs. Control subjects also exhibited TrPs (mean: 2; SD: 0.8). All were latent TrPs. Differences in the number of TrPs between both study groups were significant for active TrPs (P < 0.001), but not for latent TrPs (P > 0.5). Moreover, differences in the distribution of TrPs within the analysed cervical muscles were also significant (P < 0.01) for all muscles except for both levators capulae. All the examined muscles evoked referred pain patterns contributing to patients' symptoms. Active TrPs were more frequent in patients presenting with mechanical neck pain than in healthy subjects.
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Affiliation(s)
- C Fernández-de-las-Peñas
- Department of Physical Therapy, Occupational Therapy, Physical Medicine and Rehabilitation, Universidad Rey Juan Carlos (URJC), Alcorcón, Spain. ,
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Delgado D, Alonso-Blanco C, Fenoll C, Mena M. Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes. Ann Bot 2011; 107:1247-58. [PMID: 21447490 PMCID: PMC3101138 DOI: 10.1093/aob/mcr060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/07/2011] [Accepted: 02/10/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. METHODS Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. KEY RESULTS AND CONCLUSIONS Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and satellite lineage initiation combine in several ways. This first systematic, comprehensive natural variation survey for stomatal abundance in A. thaliana reveals cryptic developmental genetic variation, and provides relevant relationships amongst stomatal traits and extreme or uncommon accessions as resources for the genetic dissection of stomatal development.
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Affiliation(s)
- Dolores Delgado
- Departamento de Ciencias Ambientales, Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III s/n, 45071-Toledo, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, Madrid-28049, Spain
| | - Carmen Fenoll
- Departamento de Ciencias Ambientales, Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III s/n, 45071-Toledo, Spain
| | - Montaña Mena
- Departamento de Ciencias Ambientales, Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III s/n, 45071-Toledo, Spain
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Pagán I, Fraile A, Fernandez-Fueyo E, Montes N, Alonso-Blanco C, García-Arenal F. Arabidopsis thaliana as a model for the study of plant-virus co-evolution. Philos Trans R Soc Lond B Biol Sci 2010; 365:1983-95. [PMID: 20478893 PMCID: PMC2880114 DOI: 10.1098/rstb.2010.0062] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding plant-virus coevolution requires wild systems in which there is no human manipulation of either host or virus. To develop such a system, we analysed virus infection in six wild populations of Arabidopsis thaliana in Central Spain. The incidence of five virus species with different life-styles was monitored during four years, and this was analysed in relation to the demography of the host populations. Total virus incidence reached 70 per cent, which suggests a role of virus infection in the population structure and dynamics of the host, under the assumption of a host fitness cost caused by the infection. Maximum incidence occurred at early growth stages, and co-infection with different viruses was frequent, two factors often resulting in increased virulence. Experimental infections under controlled conditions with two isolates of the most prevalent viruses, cauliflower mosaic virus and cucumber mosaic virus, showed that there is genetic variation for virus accumulation, although this depended on the interaction between host and virus genotypes. Comparison of Q(ST)-based genetic differentiations between both host populations with F(ST) genetic differentiation based on putatively neutral markers suggests different selection dynamics for resistance against different virus species or genotypes. Together, these results are compatible with a hypothesis of plant-virus coevolution.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Elena Fernandez-Fueyo
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Nuria Montes
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain
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Méndez-Vigo B, de Andrés MT, Ramiro M, Martínez-Zapater JM, Alonso-Blanco C. Temporal analysis of natural variation for the rate of leaf production and its relationship with flowering initiation in Arabidopsis thaliana. J Exp Bot 2010; 61:1611-23. [PMID: 20190039 PMCID: PMC2852658 DOI: 10.1093/jxb/erq032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/22/2010] [Accepted: 01/25/2010] [Indexed: 05/19/2023]
Abstract
Vegetative growth and flowering initiation are two crucial developmental processes in the life cycle of annual plants that are closely associated. The timing of both processes affects several presumed adaptive traits, such as flowering time (FT), total leaf number (TLN), or the rate of leaf production (RLP). However, the interactions among these complex processes and traits, and their mechanistic bases, remain largely unknown. To determine the genetic relationships between them, the natural genetic variation between A. thaliana accessions Fei-0 and Ler has been studied using a new population of 222 LerxFei-0 recombinant inbred lines. Temporal analysis of the parental development under a short day photoperiod distinguishes two vegetative phases differing in their RLP. QTL mapping of RLP in consecutive time intervals of vegetative development indicates that Ler/Fei-0 variation is caused by 10 loci whose small to moderate effects mainly display two different temporal patterns. Further comparative QTL analyses show that most of the genomic regions affecting FT or TLN also alter RLP. In addition, the partially independent genetic bases observed for FT and TLN appear determined by several genomic regions with two different patterns of phenotypic effects: regions with a larger effect on FT than TLN, and vice versa. The distinct temporal and pleiotropic patterns of QTL effects suggest that natural variation for flowering time is caused by different genetic mechanisms involved in vegetative and/or reproductive phase changes, most of them interacting with the control of leaf production rate. Thus, natural selection might contribute to maintain this genetic variation due to its phenotypic effects not only on the timing of flowering initiation but also on the rate of vegetative growth.
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Affiliation(s)
| | | | | | | | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Cantoblanco, Madrid-28049, Spain
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Bentsink L, Hanson J, Hanhart CJ, Blankestijn-de Vries H, Coltrane C, Keizer P, El-Lithy M, Alonso-Blanco C, de Andrés MT, Reymond M, van Eeuwijk F, Smeekens S, Koornneef M. Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proc Natl Acad Sci U S A 2010; 107:4264-9. [PMID: 20145108 PMCID: PMC2840098 DOI: 10.1073/pnas.1000410107] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.
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Affiliation(s)
- Leónie Bentsink
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Johannes Hanson
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
| | - Corrie J. Hanhart
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | - Colin Coltrane
- Biometris–Applied Statistics, Wageningen University and Research Centre, 6708 PB Wageningen, The Netherlands
| | - Paul Keizer
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Biometris–Applied Statistics, Wageningen University and Research Centre, 6708 PB Wageningen, The Netherlands
| | - Mohamed El-Lithy
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB) and Consejo Superior de Investigaciones Científicas (CSIC), E-28049 Madrid, Spain; and
| | - M. Teresa de Andrés
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB) and Consejo Superior de Investigaciones Científicas (CSIC), E-28049 Madrid, Spain; and
| | - Matthieu Reymond
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Fred van Eeuwijk
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Biometris–Applied Statistics, Wageningen University and Research Centre, 6708 PB Wageningen, The Netherlands
| | - Sjef Smeekens
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Martín B, Ramiro M, Martínez-Zapater JM, Alonso-Blanco C. A high-density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis. BMC Plant Biol 2009; 9:147. [PMID: 20003424 PMCID: PMC2803491 DOI: 10.1186/1471-2229-9-147] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 12/14/2009] [Indexed: 05/08/2023]
Abstract
BACKGROUND Arabidopsis thaliana is the main model species for plant molecular genetics studies and world-wide efforts are devoted to identify the function of all its genes. To this end, reverse genetics by TILLING (Targeting Induced Local Lesions IN Genomes) in a permanent collection of chemically induced mutants is providing a unique resource in Columbia genetic background. In this work, we aim to extend TILLING resources available in A. thaliana by developing a new population of ethyl methanesulphonate (EMS) induced mutants in the second commonest reference strain. In addition, we pursue to saturate the number of EMS induced mutations that can be tolerated by viable and fertile plants. RESULTS By mutagenizing with different EMS concentrations we have developed a permanent collection of 3712 M2/M3 independent mutant lines in the reference strain Landsberg erecta (Ler) of A. thaliana. This population has been named as the Arabidopsis TILLer collection. The frequency of mutations per line was maximized by using M1 plants with low but sufficient seed fertility. Application of TILLING to search for mutants in 14 genes identified 21 to 46 mutations per gene, which correspond to a total of 450 mutations. Missense mutations were found for all genes while truncations were selected for all except one. We estimated that, on average, these lines carry one mutation every 89 kb, Ler population providing a total of more than five million induced mutations. It is estimated that TILLer collection shows a two to three fold higher EMS mutation density per individual than previously reported A. thaliana population. CONCLUSIONS Analysis of TILLer collection demonstrates its usefulness for large scale TILLING reverse genetics in another reference genetic background of A. thaliana. Comparisons with TILLING populations in other organisms indicate that this new A. thaliana collection carries the highest chemically induced mutation density per individual known in diploid species.
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Affiliation(s)
- Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
| | - José M Martínez-Zapater
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid-28049, Spain
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Montesinos A, Tonsor SJ, Alonso-Blanco C, Picó FX. Demographic and genetic patterns of variation among populations of Arabidopsis thaliana from contrasting native environments. PLoS One 2009; 4:e7213. [PMID: 19787050 PMCID: PMC2746291 DOI: 10.1371/journal.pone.0007213] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 08/24/2009] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana. METHODOLOGY/PRINCIPAL FINDINGS We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected. CONCLUSIONS/SIGNIFICANCE Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations.
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Affiliation(s)
- Alicia Montesinos
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephen J. Tonsor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F. Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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Pagán I, Alonso-Blanco C, García-Arenal F. Differential tolerance to direct and indirect density-dependent costs of viral infection in Arabidopsis thaliana. PLoS Pathog 2009; 5:e1000531. [PMID: 19649316 PMCID: PMC2712083 DOI: 10.1371/journal.ppat.1000531] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 07/06/2009] [Indexed: 11/19/2022] Open
Abstract
Population density and costs of parasite infection may condition the capacity of organisms to grow, survive and reproduce, i.e. their competitive ability. In host-parasite systems there are different competitive interactions: among uninfected hosts, among infected hosts, and between uninfected and infected hosts. Consequently, parasite infection results in a direct cost, due to parasitism itself, and in an indirect cost, due to modification of the competitive ability of the infected host. Theory predicts that host fitness reduction will be higher under the combined effects of costs of parasitism and competition than under each factor separately. However, experimental support for this prediction is scarce, and derives mostly from animal-parasite systems. We have analysed the interaction between parasite infection and plant density using the plant-parasite system of Arabidopsis thaliana and the generalist virus Cucumber mosaic virus (CMV). Plants of three wild genotypes grown at different densities were infected by CMV at various prevalences, and the effects of infection on plant growth and reproduction were quantified. Results demonstrate that the combined effects of host density and parasite infection may result either in a reduction or in an increase of the competitive ability of the host. The two genotypes investing a higher proportion of resources to reproduction showed tolerance to the direct cost of infection, while the genotype investing a higher proportion of resources to growth showed tolerance to the indirect cost of infection. Our findings show that the outcome of the interaction between host density and parasitism depends on the host genotype, which determines the plasticity of life-history traits and consequently, the host capacity to develop different tolerance mechanisms to the direct or indirect costs of parasitism. These results indicate the high relevance of host density and parasitism in determining the competitive ability of a plant, and stress the need to simultaneously consider both factors to understand the selective pressures that drive host-parasite co-evolution.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón (Madrid), Spain
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Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 2009; 21:1877-96. [PMID: 19574434 PMCID: PMC2729614 DOI: 10.1105/tpc.109.068114] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/10/2009] [Accepted: 06/11/2009] [Indexed: 05/17/2023]
Abstract
Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available.
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Affiliation(s)
- Carlos Alonso-Blanco
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Departamento de Genética Molecular de Plantas, Cantoblanco 28049 Madrid, Spain
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Pagán I, Alonso-Blanco C, García-Arenal F. Host responses in life-history traits and tolerance to virus infection in Arabidopsis thaliana. PLoS Pathog 2008; 4:e1000124. [PMID: 18704166 PMCID: PMC2494869 DOI: 10.1371/journal.ppat.1000124] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 07/14/2008] [Indexed: 11/19/2022] Open
Abstract
Knowing how hosts respond to parasite infection is paramount in understanding the effects of parasites on host populations and hence host–parasite co-evolution. Modification of life-history traits in response to parasitism has received less attention than other defence strategies. Life-history theory predicts that parasitised hosts will increase reproductive effort and accelerate reproduction. However, empirical analyses of these predictions are few and mostly limited to animal-parasite systems. We have analysed life-history trait responses in 18 accessions of Arabidopsis thaliana infected at two different developmental stages with three strains of Cucumber mosaic virus (CMV). Accessions were divided into two groups according to allometric relationships; these groups differed also in their tolerance to CMV infection. Life-history trait modification upon virus infection depended on the host genotype and the stage at infection. While all accessions delayed flowering, only the more tolerant allometric group modified resource allocation to increase the production of reproductive structures and progeny, and reduced the length of reproductive period. Our results are in agreement with modifications of life-history traits reported for parasitised animals and with predictions from life-history theory. Thus, we provide empirical support for the general validity of theoretical predictions. In addition, this experimental approach allowed us to quantitatively estimate the genetic determinism of life-history trait plasticity and to evaluate the role of life-history trait modification in defence against parasites, two largely unexplored issues. Hosts have developed a variety of mechanisms to compensate for the negative impact of parasite infection. Modification of life-history traits in response to parasitism has received less attention than other defence strategies. Life-history theory assumes trade-offs between resource allocation to different fitness components, and predicts that hosts under parasitism will allocate more resources to reproduction, subtracting them from those dedicated to growth and survival. Empirical support for predictions is not abundant, and derives mostly from the analysis of animal-parasite systems. We have analysed the modification of various life-history traits in the plant Arabidopsis thaliana infected by Cucumber mosaic virus. Life-history trait modification upon virus infection depended on the host genotype and on the developmental stage at infection. All plant genotypes delayed flowering, but only the more tolerant ones allocated more resources to reproduction, and reduced the length of reproductive period. These results agree with reports from parasitised animals and with predictions from life-history theory, providing empirical support for the general validity of theoretical predictions. In addition, results allow for the more precise evaluation of the role of life-history trait modification in defence against parasites by taking into account plant–virus interactions where life-history traits were differentially modified.
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Affiliation(s)
- Israel Pagán
- Departamento de Biotecnología, E.T.S.I. Agrónomos and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Fernando García-Arenal
- Departamento de Biotecnología, E.T.S.I. Agrónomos and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail:
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Pagán I, Alonso-Blanco C, García-Arenal F. The relationship of within-host multiplication and virulence in a plant-virus system. PLoS One 2007; 2:e786. [PMID: 17726516 PMCID: PMC1950075 DOI: 10.1371/journal.pone.0000786] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 07/30/2007] [Indexed: 11/24/2022] Open
Abstract
Background Virulence does not represent any obvious advantage to parasites. Most models of virulence evolution assume that virulence is an unavoidable consequence of within-host multiplication of parasites, resulting in trade-offs between within-host multiplication and between-host transmission fitness components. Experimental support for the central assumption of this hypothesis, i.e., for a positive correlation between within-host multiplication rates and virulence, is limited for plant-parasite systems. Methodology/Principal Findings We have addressed this issue in the system Arabidopsis thaliana-Cucumber mosaic virus (CMV). Virus multiplication and the effect of infection on plant growth and on viable seed production were quantified for 21 Arabidopsis wild genotypes infected by 3 CMV isolates. The effect of infection on plant growth and seed production depended of plant architecture and length of postembryonic life cycle, two genetically-determined traits, as well as on the time of infection in the plant's life cycle. A relationship between virus multiplication and virulence was not a general feature of this host-parasite system. This could be explained by tolerance mechanisms determined by the host genotype and operating differently on two components of plant fitness, biomass production and resource allocation to seeds. However, a positive relationship between virus multiplication and virulence was detected for some accessions with short life cycle and high seed weight to biomass ratio, which show lower levels of tolerance to infection. Conclusions/Significance These results show that genotype-specific tolerance mechanisms may lead to the absence of a clear relationship between parasite multiplication and virulence. Furthermore, a positive correlation between parasite multiplication and virulence may occur only in some genotypes and/or environmental conditions for a given host-parasite system. Thus, our results challenge the general validity of the trade-off hypothesis for virulence evolution, and stress the need of considering the effect of both the host and parasite genotypes in analyses of host-parasite interactions.
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Affiliation(s)
- Israel Pagán
- Departamento de Biotecnología and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma, Cantoblanco, Madrid, Spain
| | - Fernando García-Arenal
- Departamento de Biotecnología and Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain
- * To whom correspondence should be addressed. E-mail:
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Jiménez-Gómez JM, Alonso-Blanco C, Borja A, Anastasio G, Angosto T, Lozano R, Martínez-Zapater JM. Quantitative genetic analysis of flowering time in tomato. Genome 2007; 50:303-15. [PMID: 17502904 DOI: 10.1139/g07-009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial selection of cultivated tomato (Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii. Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.
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Affiliation(s)
- José M Jiménez-Gómez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Keurentjes JJB, Bentsink L, Alonso-Blanco C, Hanhart CJ, Blankestijn-De Vries H, Effgen S, Vreugdenhil D, Koornneef M. Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics 2006; 175:891-905. [PMID: 17179089 PMCID: PMC1800614 DOI: 10.1534/genetics.106.066423] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.
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Affiliation(s)
- Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, NL-6703 BD, Wageningen, The Netherlands
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Abstract
The study of the intraspecific natural variation existing in Arabidopsis provides a useful resource for the dissection of its genome at the functional, ecological, and evolutionary levels. A major step in these studies is the identification and location of quantitative trait loci (QTLs) determining the variation for trait(s) of interest, so-called QTL analysis. Here we provide general methods to achieve this goal, including (1) the selection of wild accessions that can serve as parental lines for QTL mapping; (2) the development of mapping populations; (3) the construction of the required genome-wide linkage maps of the populations; and (4) the mapping and characterization of QTLs affecting the trait(s).
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Affiliation(s)
- Carlos Alonso-Blanco
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Centro Nacional de Biotecnologiá (CNB), CSIC, Cantoblanco, Madrid, Spain
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Fernández-de-las-Peñas C, Alonso-Blanco C, Cuadrado ML, Pareja JA. Forward head posture and neck mobility in chronic tension-type headache: a blinded, controlled study. Cephalalgia 2006; 26:314-9. [PMID: 16472338 DOI: 10.1111/j.1468-2982.2005.01042.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Forward head posture (FHP) and neck mobility were objectively assessed in 25 patients with chronic tension-type headache (CTTH) and 25 healthy controls. Side-view pictures were taken in a sitting position to measure the cranio-vertebral angle. A cervical goniometer was employed to measure the range of all cervical motions. Patients with CTTH showed a smaller cranio-vertebral angle (45.3 degrees +/- 7.6 degrees) than controls (54.1 degrees +/- 6.3 degrees), thus presenting a greater FHP (P < 0.001). Patients also had lesser neck mobility for all cervical movements, except for right lateral flexion (P < 0.01). There was a positive correlation between the cranio-vertebral angle and neck mobility. Within the CTTH group, a negative correlation was found between the cranio-vertebral angle and headache frequency, but neck mobility did not correlate with headache parameters. Further research is needed to define a potential role of FHP and restricted neck mobility in the origin or maintenance of TTH.
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Affiliation(s)
- C Fernández-de-las-Peñas
- Department of Physical Therapy & Occupational Therapy, Physical Medicine and Rehabilitation of Universidad Rey Juan Carlos, Alcorcón, Madrid, Spain.
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