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Hartfield M, Glémin S. Polygenic selection to a changing optimum under self-fertilisation. PLoS Genet 2024; 20:e1011312. [PMID: 39018328 DOI: 10.1371/journal.pgen.1011312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/29/2024] [Accepted: 05/21/2024] [Indexed: 07/19/2024] Open
Abstract
Many traits are polygenic, affected by multiple genetic variants throughout the genome. Selection acting on these traits involves co-ordinated allele-frequency changes at these underlying variants, and this process has been extensively studied in random-mating populations. Yet many species self-fertilise to some degree, which incurs changes to genetic diversity, recombination and genome segregation. These factors cumulatively influence how polygenic selection is realised in nature. Here, we use analytical modelling and stochastic simulations to investigate to what extent self-fertilisation affects polygenic adaptation to a new environment. Our analytical solutions show that while selfing can increase adaptation to an optimum, it incurs linkage disequilibrium that can slow down the initial spread of favoured mutations due to selection interference, and favours the fixation of alleles with opposing trait effects. Simulations show that while selection interference is present, high levels of selfing (at least 90%) aids adaptation to a new optimum, showing a higher long-term fitness. If mutations are pleiotropic then only a few major-effect variants fix along with many neutral hitchhikers, with a transient increase in linkage disequilibrium. These results show potential advantages to self-fertilisation when adapting to a new environment, and how the mating system affects the genetic composition of polygenic selection.
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Affiliation(s)
- Matthew Hartfield
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sylvain Glémin
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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2
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Xu F, Dong H, Guo W, Le L, Jing Y, Fletcher JC, Sun J, Pu L. The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes. PLANT COMMUNICATIONS 2024; 5:100819. [PMID: 38217289 PMCID: PMC11009162 DOI: 10.1016/j.xplc.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis. Loss of ULT1 function significantly increases rosette leaf, petal, silique, and seed size, whereas overexpression of ULT1 results in reduced organ size. ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication. Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development. ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes, activating their expression to determine final cell size. Furthermore, we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation. Collectively, our findings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA 94710, USA
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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3
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Frachon L, Schiestl FP. Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution. BMC Ecol Evol 2024; 24:7. [PMID: 38195402 PMCID: PMC10775529 DOI: 10.1186/s12862-023-02194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Insect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes remain largely unknown despite their importance in predicting adaptive responses to natural or to artificial selection. Based on a nine-generation experimental evolution study with fast cycling Brassica rapa plants adapting to bumblebees, we investigate the genomic evolution associated with the previously observed parallel phenotypic evolution. In this current evolve and resequencing (E&R) study, we conduct a genomic scan of the allele frequency changes along the genome in bumblebee-pollinated and hand-pollinated plants and perform a genomic principal component analysis (PCA). RESULTS We highlight rapid genomic evolution associated with the observed phenotypic evolution mediated by bumblebees. Controlling for genetic drift, we observe significant changes in allelic frequencies at multiple loci. However, this pattern differs according to the replicate of bumblebee-pollinated plants, suggesting putative non-parallel genomic evolution. Finally, our study underlines an increase in genomic variance implying the putative involvement of multiple loci in short-term pollinator adaptation. CONCLUSIONS Overall, our study enhances our understanding of the complex interactions between pollinator and plants, providing a stepping stone towards unravelling the genetic basis of plant genomic adaptation to biotic factors in the environment.
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Affiliation(s)
- Léa Frachon
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland.
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
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4
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Yuan W, Beitel F, Srikant T, Bezrukov I, Schäfer S, Kraft R, Weigel D. Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids. Genome Biol 2023; 24:200. [PMID: 37667232 PMCID: PMC10478501 DOI: 10.1186/s13059-023-03043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we turn to hybrids, which provide a facile means for creating many novel allele combinations. RESULTS We focus on the interaction between alleles of the same locus, i.e., dominance, and perform a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive, dominant gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below the parental average. Unlike in the additive genes, regulatory rare-allele burden in the dominant gene set is strongly correlated with F1 rosette size, even though it only mildly covaries with the expression level of these genes. CONCLUSIONS Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.
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Affiliation(s)
- Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Fiona Beitel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Sabine Schäfer
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Robin Kraft
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076, Tübingen, Germany.
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5
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Wuest SE, Schulz L, Rana S, Frommelt J, Ehmig M, Pires ND, Grossniklaus U, Hardtke CS, Hammes UZ, Schmid B, Niklaus PA. Single-gene resolution of diversity-driven overyielding in plant genotype mixtures. Nat Commun 2023; 14:3379. [PMID: 37291153 PMCID: PMC10250416 DOI: 10.1038/s41467-023-39130-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.
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Affiliation(s)
- Samuel E Wuest
- Department of Evolutionary Biology and Environmental Studies and Zurich-Basel Plant Science Center, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
- Department of Geography, Remote Sensing Laboratories, University of Zurich, 8057, Zurich, Switzerland.
- Agroscope, Group Breeding Research, Mueller-Thurgau-Strasse 29, 8820, Waedenswil, Switzerland.
| | - Lukas Schulz
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Ln, Norwich, NR4 7UH, United Kingdom
| | - Julia Frommelt
- Department of Evolutionary Biology and Environmental Studies and Zurich-Basel Plant Science Center, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Merten Ehmig
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Nuno D Pires
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Ulrich Z Hammes
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies and Zurich-Basel Plant Science Center, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Geography, Remote Sensing Laboratories, University of Zurich, 8057, Zurich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies and Zurich-Basel Plant Science Center, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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6
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Wuest SE, Pires ND, Luo S, Vasseur F, Messier J, Grossniklaus U, Niklaus PA. Increasing plant group productivity through latent genetic variation for cooperation. PLoS Biol 2022; 20:e3001842. [PMID: 36445870 PMCID: PMC9707777 DOI: 10.1371/journal.pbio.3001842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that-while beneficial to the group-decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.
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Affiliation(s)
- Samuel E. Wuest
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland,Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland,Group Breeding Research, Division Plant Breeding, Agroscope, Wädenswil, Switzerland,* E-mail:
| | - Nuno D. Pires
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Shan Luo
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Julie Messier
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Pascal A. Niklaus
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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7
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Clauw P, Kerdaffrec E, Gunis J, Reichardt-Gomez I, Nizhynska V, Koemeda S, Jez J, Nordborg M. Locally adaptive temperature response of vegetative growth in Arabidopsis thaliana. eLife 2022; 11:e77913. [PMID: 35904422 PMCID: PMC9337855 DOI: 10.7554/elife.77913] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/13/2022] [Indexed: 02/06/2023] Open
Abstract
We investigated early vegetative growth of natural Arabidopsis thaliana accessions in cold, nonfreezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes. We found that accessions from northern latitudes produced larger seedlings than accessions from southern latitudes, partly as a result of larger seed size. However, their subsequent vegetative growth when exposed to colder temperatures was slower. The difference was too large to be explained by random population differentiation, and is thus suggestive of local adaptation, a notion that is further supported by substantial transcriptome and metabolome changes in northern accessions. We hypothesize that the reduced growth of northern accessions is an adaptive response and a consequence of reallocating resources toward cold acclimation and winter survival.
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Affiliation(s)
- Pieter Clauw
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Envel Kerdaffrec
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Joanna Gunis
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | | | - Viktoria Nizhynska
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Stefanie Koemeda
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbHViennaAustria
| | - Jakub Jez
- Plant Sciences Facility, Vienna BioCenter Core Facilities GmbHViennaAustria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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8
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Valenza-Troubat N, Montanari S, Ritchie P, Wellenreuther M. Unraveling the complex genetic basis of growth in New Zealand silver trevally ( Pseudocaranx georgianus). G3 GENES|GENOMES|GENETICS 2022; 12:6512062. [PMID: 35100394 PMCID: PMC8896004 DOI: 10.1093/g3journal/jkac016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/06/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally.
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Affiliation(s)
- Noemie Valenza-Troubat
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
| | - Sara Montanari
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
| | - Peter Ritchie
- School of Biological Sciences, Victoria University of Wellington , Wellington 6140, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
- School of Biological Sciences, The University of Auckland , Auckland 1010, New Zealand
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9
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Bataillon T, Gauthier P, Villesen P, Santoni S, Thompson JD, Ehlers BK. From genotype to phenotype: Genetic redundancy and the maintenance of an adaptive polymorphism in the context of high gene flow. Evol Lett 2022; 6:189-202. [PMID: 35386834 PMCID: PMC8966474 DOI: 10.1002/evl3.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/23/2021] [Accepted: 01/16/2022] [Indexed: 11/11/2022] Open
Abstract
A central question in evolution is how several adaptive phenotypes are maintained within a species. Theory predicts that the genetic determination of a trait, and in particular the amounts of redundancy in the mapping of genotypes to phenotypes, mediates evolutionary outcomes of phenotypic selection. In Mediterranean wild thyme, numerous discrete chemical phenotypes (chemotypes) occur in close geographic proximity. Chemotypes are defined by the predominant monoterpene produced by individual plants in their essential oil. In this study, we analyze the ecological genetics of six chemotypes nested within two well‐established chemical families (hereafter ecotypes). Ecotypes, and chemotypes within ecotypes, are spatially segregated, and their distributions track local differences in the abiotic environment. By combining population genomic, phenotypic, and environmental data from 700 individuals, we show how the genetics of ecotype determination mediates this evolutionary response. Variation in three terpene‐synthase loci explains variation in ecotype identity, with one single locus accounting for as much as 78% of this variation. Phenotypic selection combined with low segregating genotypic redundancy of ecotypes leaves a clear footprint at the genomic level: alleles associated with ecotype identity track environmental variation despite extensive gene flow. Different chemotypes within each ecotype differentially track environmental variation. Their identity is determined by multiple loci and displays a wider range of genotypic redundancy that dilutes phenotypic selection on their characteristic alleles. Our study thus provides a novel illustration of how genetic redundancy of a phenotype modulates the ability of selection to maintain adaptive differentiation. Identifying the precise genetics of the chemical polymorphism in thyme is the next crucial step for our understanding of the origin and maintenance of a polymorphism that is present in many aromatic plants.
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Affiliation(s)
- Thomas Bataillon
- Bioinformatics Research Center Aarhus University Aarhus 8000 Denmark
| | - Perrine Gauthier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier 34293 France
| | - Palle Villesen
- Bioinformatics Research Center Aarhus University Aarhus 8000 Denmark
| | - Sylvain Santoni
- UMR AGAP Institut Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier 34398 France
| | - John D. Thompson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier 34293 France
| | - Bodil K. Ehlers
- Department of Ecoscience Aarhus University Silkeborg 8600 Denmark
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10
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Morón-García O, Garzón-Martínez GA, Martínez-Martín MJP, Brook J, Corke FMK, Doonan JH, Camargo Rodríguez AV. Genetic architecture of variation in Arabidopsis thaliana rosettes. PLoS One 2022; 17:e0263985. [PMID: 35171969 PMCID: PMC8849614 DOI: 10.1371/journal.pone.0263985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/01/2022] [Indexed: 12/04/2022] Open
Abstract
Rosette morphology across Arabidopsis accessions exhibits considerable variation. Here we report a high-throughput phenotyping approach based on automatic image analysis to quantify rosette shape and dissect the underlying genetic architecture. Shape measurements of the rosettes in a core set of Recombinant Inbred Lines from an advanced mapping population (Multiparent Advanced Generation Inter-Cross or MAGIC) derived from inter-crossing 19 natural accessions. Image acquisition and analysis was scaled to extract geometric descriptors from time stamped images of growing rosettes. Shape analyses revealed heritable morphological variation at early juvenile stages and QTL mapping resulted in over 116 chromosomal regions associated with trait variation within the population. Many QTL linked to variation in shape were located near genes related to hormonal signalling and signal transduction pathways while others are involved in shade avoidance and transition to flowering. Our results suggest rosette shape arises from modular integration of sub-organ morphologies and can be considered a functional trait subjected to selective pressures of subsequent morphological traits. On an applied aspect, QTLs found will be candidates for further research on plant architecture.
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Affiliation(s)
- Odín Morón-García
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Gina A. Garzón-Martínez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - M. J. Pilar Martínez-Martín
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jason Brook
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Fiona M. K. Corke
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
| | - Anyela V. Camargo Rodríguez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
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11
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Hartfield M, Poulsen NA, Guldbrandtsen B, Bataillon T. Using singleton densities to detect recent selection in Bos taurus. Evol Lett 2021; 5:595-606. [PMID: 34917399 PMCID: PMC8645200 DOI: 10.1002/evl3.263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/05/2022] Open
Abstract
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the "Singleton Density Score" (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans-milk protein content, milk fat content, and stature-have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.
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Affiliation(s)
- Matthew Hartfield
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and GeneticsAarhus UniversityTjeleDK‐8830Denmark
- Rheinische Friedrich‐Wilhelms‐Universität BonnInstitut für TierwissenschaftenBonnDE‐53115Germany
- Department of Veterinary SciencesCopenhagen UniversityFrederiksberg CDK‐1870Denmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
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