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Theißen G, Rümpler F, Gramzow L. Array of MADS-Box Genes: Facilitator for Rapid Adaptation? TRENDS IN PLANT SCIENCE 2018; 23:563-576. [PMID: 29802068 DOI: 10.1016/j.tplants.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
Abstract
In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.
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Affiliation(s)
- Günter Theißen
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany.
| | - Florian Rümpler
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
| | - Lydia Gramzow
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Philosophenweg 12, D-07743 Jena, Germany
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2
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Taylor MA, Cooper MD, Sellamuthu R, Braun P, Migneault A, Browning A, Perry E, Schmitt J. Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field. THE NEW PHYTOLOGIST 2017; 216:291-302. [PMID: 28752957 DOI: 10.1111/nph.14712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations.
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Affiliation(s)
- Mark A Taylor
- University of California at Davis, Davis, CA, 95616, USA
| | | | | | - Peter Braun
- Brown University, Providence, RI, 02912, USA
- California State University at San Bernardino, San Bernardino, CA, 92407, USA
| | | | | | - Emily Perry
- Brown University, Providence, RI, 02912, USA
| | - Johanna Schmitt
- University of California at Davis, Davis, CA, 95616, USA
- Brown University, Providence, RI, 02912, USA
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Abstract
Darwin's theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.
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Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria;
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4
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Postma FM, Ågren J. Maternal environment affects the genetic basis of seed dormancy inArabidopsis thaliana. Mol Ecol 2015; 24:785-97. [DOI: 10.1111/mec.13061] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/16/2014] [Accepted: 12/30/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Froukje M. Postma
- Department of Plant Ecology and Evolution; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18 D SE-752 36 Uppsala Sweden
| | - Jon Ågren
- Department of Plant Ecology and Evolution; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18 D SE-752 36 Uppsala Sweden
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5
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Suter L, Rüegg M, Zemp N, Hennig L, Widmer A. Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. PLANT PHYSIOLOGY 2014; 166:1928-42. [PMID: 25339407 PMCID: PMC4256870 DOI: 10.1104/pp.114.247346] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800-2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation.
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Affiliation(s)
- Léonie Suter
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Marlene Rüegg
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Niklaus Zemp
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Lars Hennig
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
| | - Alex Widmer
- Eidgenössisch Technische Hochschule Zürich, Institute of Integrative Biology, 8092 Zurich, Switzerland (L.S., M.R., N.Z., A.W.); andDepartment of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden (L.H.)
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DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination. Proc Natl Acad Sci U S A 2014; 111:E3571-80. [PMID: 25114251 DOI: 10.1073/pnas.1403851111] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seed germination is an important life-cycle transition because it determines subsequent plant survival and reproductive success. To detect optimal spatiotemporal conditions for germination, seeds act as sophisticated environmental sensors integrating information such as ambient temperature. Here we show that the delay of germination 1 (DOG1) gene, known for providing dormancy adaptation to distinct environments, determines the optimal temperature for seed germination. By reciprocal gene-swapping experiments between Brassicaceae species we show that the DOG1-mediated dormancy mechanism is conserved. Biomechanical analyses show that this mechanism regulates the material properties of the endosperm, a seed tissue layer acting as germination barrier to control coat dormancy. We found that DOG1 inhibits the expression of gibberellin (GA)-regulated genes encoding cell-wall remodeling proteins in a temperature-dependent manner. Furthermore we demonstrate that DOG1 causes temperature-dependent alterations in the seed GA metabolism. These alterations in hormone metabolism are brought about by the temperature-dependent differential expression of genes encoding key enzymes of the GA biosynthetic pathway. These effects of DOG1 lead to a temperature-dependent control of endosperm weakening and determine the optimal temperature for germination. The conserved DOG1-mediated coat-dormancy mechanism provides a highly adaptable temperature-sensing mechanism to control the timing of germination.
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Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: searching for G×E effects. G3-GENES GENOMES GENETICS 2014; 4:1465-78. [PMID: 24902604 PMCID: PMC4132177 DOI: 10.1534/g3.114.012427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the natural world, genotype expression is influenced by an organism’s environment. Identifying and understanding the genes underlying phenotypes in different environments is important for making advances in fields ranging from evolution to medicine to agriculture. With the availability of genome-wide genetic-marker datasets, it is possible to look for genes that interact with the environment. Using the model organism, Arabidopsis thaliana, we looked for genes underlying phenotypes as well as genotype-by-environment interactions in four germination traits under two light and two nutrient conditions. We then performed genome-wide association tests to identify candidate genes underlying the observed phenotypes and genotype-by-environment interactions. Of the four germination traits examined, only two showed significant genotype-by-environment interactions. While genome-wide association analyses did not identify any markers or genes explicitly linked to genotype-by-environment interactions, we did identify a total of 55 markers and 71 genes associated with germination differences. Of the 71 genes, four—ZIGA4, PS1, TOR, and TT12—appear to be strong candidates for further study of germination variation under different environments.
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Huang X, Ding J, Effgen S, Turck F, Koornneef M. Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis. THE NEW PHYTOLOGIST 2013; 199:843-57. [PMID: 23668187 DOI: 10.1111/nph.12306] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 05/02/2023]
Abstract
Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control.
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Affiliation(s)
- Xueqing Huang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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Yano R, Takebayashi Y, Nambara E, Kamiya Y, Seo M. Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:815-28. [PMID: 23464703 DOI: 10.1111/tpj.12167] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/20/2013] [Accepted: 02/27/2013] [Indexed: 05/20/2023]
Abstract
Seed dormancy is an important adaptive trait that enables germination at the proper time, thereby ensuring plant survival after germination. In Arabidopsis, considerable variation exists in the degree of seed dormancy among wild-type accessions (ecotypes). In this paper, we identify a plant-specific HD2 histone deacetylase gene, HD2B (At5g22650), as a genetic factor associated with seed dormancy. First, genome-wide association mapping of 113 accessions was used to identify single nucleotide polymorphisms that possibly explain natural variation for seed dormancy. Integration of genome-wide association mapping and transcriptome analysis during cold-induced dormancy cycling identified HD2B as the most plausible candidate gene, and quantitative RT-PCR analysis demonstrated that HD2B expression was up-regulated by cold and after-ripening (dry storage of mature seed), treatments that are known to break seed dormancy. Interestingly, quantitative RT-PCR analysis in 106 accessions revealed that the expression of HD2B in imbibed seeds was significantly suppressed in most of the dormant accessions compared with less-dormant accessions, suggesting that suppression of HD2B expression may be important to maintain seed dormancy in dormant accessions. In addition, transgenic seeds of a dormant Cvi-0 accession that carried a 2.5 kb genomic DNA fragment of HD2B cloned from a less-dormant Col-0 accession ((Col)HD2B/Cvi-0) exhibited reduced seed dormancy accompanied by enhanced expression of HD2B when after-ripened or cold-imbibed. Endogenous levels of gibberellin were found to be increased in the imbibed seeds of after-ripened (Col)HD2B/Cvi-0 compared with wild-type Cvi-0. These results suggest that HD2B plays a role in seed dormancy and/or germinability in Arabidopsis thaliana.
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Affiliation(s)
- Ryoichi Yano
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.
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