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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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2
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Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Yuan Y, Du Y, Delaplace P. Unraveling the molecular mechanisms governing axillary meristem initiation in plants. PLANTA 2024; 259:101. [PMID: 38536474 DOI: 10.1007/s00425-024-04370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/22/2024] [Indexed: 04/24/2024]
Abstract
MAIN CONCLUSION Axillary meristems (AMs) located in the leaf axils determine the number of shoots or tillers eventually formed, thus contributing significantly to the plant architecture and crop yields. The study of AM initiation is unavoidable and beneficial for crop productivity. Shoot branching is an undoubted determinant of plant architecture and thus greatly impacts crop yield due to the panicle-bearing traits of tillers. The emergence of the AM is essential for the incipient bud formation, and then the bud is dormant or outgrowth immediately to form a branch or tiller. While numerous reviews have focused on plant branching and tillering development networks, fewer specifically address AM initiation and its regulatory mechanisms. This review synthesizes the significant advancements in the genetic and hormonal factors governing AM initiation, with a primary focus on studies conducted in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). In particular, by elaborating on critical genes like LATERAL SUPPRESSOR (LAS), which specifically regulates AM initiation and the networks in which they are involved, we attempt to unify the cascades through which they are positioned. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Additionally, we examine challenges in elucidating AM formation mechanisms alongside opportunities provided by emerging omics approaches to identify AM-specific genes. By expanding our comprehension of the genetic and hormonal regulation of AM development, we can develop strategies to optimize crop production and address global food challenges effectively.
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Affiliation(s)
- Yundong Yuan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Yanfang Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Pierre Delaplace
- Plant Sciences, Gembloux Agro-Bio Tech, TERRA-Teaching and Research Center, Université de Liège, 5030, Gembloux, Belgium
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Novikova PY, Kolesnikova UK, Scott AD. Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. PLANT REPRODUCTION 2023; 36:125-138. [PMID: 36282331 PMCID: PMC9957919 DOI: 10.1007/s00497-022-00451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 05/15/2023]
Abstract
Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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Affiliation(s)
- Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.
| | - Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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5
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Ferrero-Serrano Á, Sylvia MM, Forstmeier PC, Olson AJ, Ware D, Bevilacqua PC, Assmann SM. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biol 2022; 23:101. [PMID: 35440059 PMCID: PMC9017077 DOI: 10.1186/s13059-022-02656-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.” Results We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. Conclusion We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02656-4.
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Affiliation(s)
- Ángel Ferrero-Serrano
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Megan M Sylvia
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Peter C Forstmeier
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Andrew J Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA. .,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
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6
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Estarague A, Vasseur F, Sartori K, Bastias CC, Cornet D, Rouan L, Beurier G, Exposito-Alonso M, Herbette S, Bresson J, Vile D, Violle C. Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana? ANNALS OF BOTANY 2022; 129:343-356. [PMID: 34918027 PMCID: PMC8835660 DOI: 10.1093/aob/mcab149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species' ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies from the CSR scheme and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center- margins gradient within the native range of Arabidopsis thaliana. METHODS We experimentally examined the phenotypic outcomes of plant adaptation at the center and margins of its geographic range using 30 accessions from southern, central and northern Europe. We characterized the variation of traits related to stress tolerance, resource use, colonization ability, CSR strategy scores, survival and fecundity in response to high temperature (34 °C) or frost (- 6 °C), combined with a water deficit treatment. KEY RESULTS We found evidence for both a latitudinal and a center-margins differentiation for the traits under scrutiny. Age at maturity, leaf dry matter content, specific leaf area and leaf nitrogen content varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Leaf area, C-scores, R-scores and fruit number followed a center-margins differentiation. Central accessions displayed a higher phenotypic plasticity than northern and southern accessions for most studied traits. CONCLUSIONS Traits related to an acquisitive/conservative resource-use trade-off followed a latitudinal gradient. Traits associated with a competition/colonization trade-off differentiated along the historic colonization of the distribution range and then followed a center-margins differentiation. Our findings pinpoint the need to consider the joint effect of evolutionary history and environmental factors when examining phenotypic variation across the distribution range of a species.
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Affiliation(s)
- Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRAE, Montpellier SupAgro, UMR759, F-34060, Montpellier, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
| | - Kevin Sartori
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Denis Cornet
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Gregory Beurier
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Justine Bresson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
| | - Denis Vile
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRAE, Montpellier SupAgro, UMR759, F-34060, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, F-34293, Montpellier, France
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7
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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8
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Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana. Nat Commun 2020; 11:4140. [PMID: 32811829 PMCID: PMC7435183 DOI: 10.1038/s41467-020-17896-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/16/2020] [Indexed: 01/06/2023] Open
Abstract
Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to their environment. Applying classical quantitative genetics on a segregating population derived from a Can-0xCol-0 cross, we identify the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation in plant growth and color. We show that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation, observable across thousands of plant species. Functional differences at FLM rely on a single intronic substitution, disturbing transcript splicing and leading to the accumulation of non-functional FLM transcripts. Associations between this substitution and phenotypic and climatic data across Arabidopsis natural populations, show how noncoding genetic variation at a single gene might be adaptive through pleiotropic effects. FLOWERING LOCUS M (FLM) is known as a repressor of Arabidopsis flowering. Here, the authors show that a single intronic substitution of FLM modulates leaf color and plant growth strategy along the leaf economics spectrum, as well as plays a role in plant adaptation.
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Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:2526-2534. [PMID: 31964817 PMCID: PMC7007534 DOI: 10.1073/pnas.1912451117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The seasonal timing of seed germination is critical for plant fitness in different climates. To germinate at the right time of year, seeds respond to seasonal environmental cues, such as cold temperatures. We characterized genetic variation in seed dormancy responses to cold across the geographic range of a widespread annual plant. Induction of secondary seed dormancy during winter conditions (which restricts germination to autumn) was positively correlated with flowering time, constructing winter and spring seasonal life-history strategies. Variation in seed chilling responses was strongly associated with functional variants of a known dormancy gene. These variants showed evidence of ancient diversification associated with Pleistocene glacial cycles, and were associated with climate gradients across the species’ geographical range. The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.
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10
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Greenbaum G, Rubin A, Templeton AR, Rosenberg NA. Network-based hierarchical population structure analysis for large genomic data sets. Genome Res 2019; 29:2020-2033. [PMID: 31694865 PMCID: PMC6886512 DOI: 10.1101/gr.250092.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/01/2019] [Indexed: 01/24/2023]
Abstract
Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.
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Affiliation(s)
- Gili Greenbaum
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Amir Rubin
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er-Sheva, 8410501, Israel
| | - Alan R Templeton
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa, 31905, Israel
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, California 94305, USA
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