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Desbiez-Piat A, Ressayre A, Marchadier E, Noly A, Remoué C, Vitte C, Belcram H, Bourgais A, Galic N, Le Guilloux M, Tenaillon MI, Dillmann C. Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics 2023; 225:iyad186. [PMID: 37824828 DOI: 10.1093/genetics/iyad186] [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: 07/27/2023] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.
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Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
- Université Montpellier, INRAE, Institut Agro Montpellier, LEPSE, Montpellier 34000, France
| | - Adrienne Ressayre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Elodie Marchadier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Alicia Noly
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institut of Plants Sciences Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Clémentine Vitte
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Harry Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Aurélie Bourgais
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Nathalie Galic
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
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Plancade S, Marchadier E, Huet S, Ressayre A, Noûs C, Dillmann C. A successive time-to-event model of phyllochron dynamics for hypothesis testing: application to the analysis of genetic and environmental effects in maize. PLANT METHODS 2023; 19:54. [PMID: 37287031 PMCID: PMC10245529 DOI: 10.1186/s13007-023-01029-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 05/09/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND The time between the appearance of successive leaves, or phyllochron, characterizes the vegetative development of annual plants. Hypothesis testing models, which allow the comparison of phyllochrons between genetic groups and/or environmental conditions, are usually based on regression of thermal time on the number of leaves; most of the time a constant leaf appearance rate is assumed. However regression models ignore auto-correlation of the leaf number process and may lead to biased testing procedures. Moreover, the hypothesis of constant leaf appearance rate may be too restrictive. METHODS We propose a stochastic process model in which emergence of new leaves is considered to result from successive time-to-events. This model provides a flexible and more accurate modeling as well as unbiased testing procedures. It was applied to an original maize dataset collected in the field over three years on plants originating from two divergent selection experiments for flowering time in two maize inbred lines. RESULTS AND CONCLUSION We showed that the main differences in phyllochron were not observed between selection populations but rather between ancestral lines, years of experimentation and leaf ranks. Our results highlight a strong departure from the assumption of a constant leaf appearance rate over a season which could be related to climate variations, even if the impact of individual climate variables could not be clearly determined.
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Affiliation(s)
- Sandra Plancade
- UR MIAT, University of Toulouse, INRAE, 31320 Castanet-Tolosan, France
| | - Elodie Marchadier
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12 route 128, 91190 Gif-sur-Yvette, France
| | - Sylvie Huet
- MaIAGE, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France
| | - Adrienne Ressayre
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12 route 128, 91190 Gif-sur-Yvette, France
| | - Camille Noûs
- Cogitamus Laboratory, 31320 Castanet-Tolosan, France
| | - Christine Dillmann
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12 route 128, 91190 Gif-sur-Yvette, France
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Kronholm I. Evolution of anticipatory effects mediated by epigenetic changes. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac007. [PMID: 35475265 PMCID: PMC9031056 DOI: 10.1093/eep/dvac007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 05/20/2023]
Abstract
Anticipatory effects mediated by epigenetic changes occur when parents modify the phenotype of their offspring by making epigenetic changes in their gametes, guided by information from an environmental cue. To investigate when do anticipatory effects mediated by epigenetic changes evolve in a fluctuating environment, I use an individual-based simulation model with explicit genetic architecture. The model allows for the population to respond to environmental changes by evolving plasticity, bet hedging, or by tracking the environment with genetic adaptation, in addition to the evolution of anticipatory effects. The results show that anticipatory effects evolve when the environmental cue provides reliable information about the environment and the environment changes at intermediate rates, provided that fitness costs of anticipatory effects are rather low. Moreover, evolution of anticipatory effects is quite robust to different genetic architectures when reliability of the environmental cue is high. Anticipatory effects always give smaller fitness benefits than within-generation plasticity, suggesting a possible reason for generally small observed anticipatory effects in empirical studies.
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Affiliation(s)
- Ilkka Kronholm
- *Correspondence address. Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland. Tel: +358 14 617 239; Fax: +358 14 617 239; E-mail:
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Desbiez-Piat A, Le Rouzic A, Tenaillon MI, Dillmann C. Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations. Genetics 2021; 219:6339583. [PMID: 34849881 DOI: 10.1093/genetics/iyab123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Population and quantitative genetic models provide useful approximations to predict long-term selection responses sustaining phenotypic shifts, and underlying multilocus adaptive dynamics. Valid across a broad range of parameters, their use for understanding the adaptive dynamics of small selfing populations undergoing strong selection intensity (thereafter High Drift-High selection regime, HDHS) remains to be explored. Saclay Divergent Selection Experiments (DSEs) on maize flowering time provide an interesting example of populations evolving under HDHS, with significant selection responses over 20 generations in two directions. We combined experimental data from Saclay DSEs, forward individual-based simulations, and theoretical predictions to dissect the evolutionary mechanisms at play in the observed selection responses. We asked two main questions: How do mutations arise, spread, and reach fixation in populations evolving under HDHS? How does the interplay between drift and selection influence observed phenotypic shifts? We showed that the long-lasting response to selection in small populations is due to the rapid fixation of mutations occurring during the generations of selection. Among fixed mutations, we also found a clear signal of enrichment for beneficial mutations revealing a limited cost of selection. Both environmental stochasticity and variation in selection coefficients likely contributed to exacerbate mutational effects, thereby facilitating selection grasp and fixation of small-effect mutations. Together our results highlight that despite a small number of polymorphic loci expected under HDHS, adaptive variation is continuously fueled by a vast mutational target. We discuss our results in the context of breeding and long-term survival of small selfing populations.
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Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91120 Gif-sur-Yvette, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
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Technow F, Podlich D, Cooper M. Back to the future: Implications of genetic complexity for the structure of hybrid breeding programs. G3 (BETHESDA, MD.) 2021; 11:6265599. [PMID: 33950172 PMCID: PMC8495936 DOI: 10.1093/g3journal/jkab153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022]
Abstract
Commercial hybrid breeding operations can be described as decentralized networks of smaller, more or less isolated breeding programs. There is further a tendency for the disproportionate use of successful inbred lines for generating the next generation of recombinants, which has led to a series of significant bottlenecks, particularly in the history of the North American and European maize germplasm. Both the decentralization and the disproportionate contribution of inbred lines reduce effective population size and constrain the accessible genetic space. Under these conditions, long-term response to selection is not expected to be optimal under the classical infinitesimal model of quantitative genetics. In this study, we therefore aim to propose a rationale for the success of large breeding operations in the context of genetic complexity arising from the structure and properties of interactive genetic networks. For this, we use simulations based on the NK model of genetic architecture. We indeed found that constraining genetic space through program decentralization and disproportionate contribution of parental inbred lines, is required to expose additive genetic variation and thus facilitate heritable genetic gains under high levels of genetic complexity. These results introduce new insights into why the historically grown structure of hybrid breeding programs was successful in improving the yield potential of hybrid crops over the last century. We also hope that a renewed appreciation for “why things worked” in the past can guide the adoption of novel technologies and the design of future breeding strategies for navigating biological complexity.
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Affiliation(s)
- Frank Technow
- Plant Breeding, Corteva Agriscience, Tavistock, ON, N0B 2R0, Canada
| | - Dean Podlich
- Systems and Innovation for Breeding and Seed Products, Corteva Agriscience, Johnston, IA, 50131, USA
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4067, Australia
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David O, Le Rouzic A, Dillmann C. Optimization of sampling designs for pedigrees and association studies. Biometrics 2021; 78:1056-1066. [PMID: 33876835 DOI: 10.1111/biom.13476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/10/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
In many studies, related individuals are phenotyped in order to infer how their genotype contributes to their phenotype, through the estimation of parameters such as breeding values or locus effects. When it is not possible to phenotype all the individuals, it is important to properly sample the population to improve the precision of the statistical analysis. This article studies how to optimize such sampling designs for pedigrees and association studies. Two sampling methods are developed, stratified sampling and D optimality. It is found that it is important to take account of mutation when sampling pedigrees with many generations: as the size of mutation effects increases, optimized designs sample more individuals in late generations. Optimized designs for association studies tend to improve the joint estimation of breeding values and locus effects, all the more as sample size is low and the genetic architecture of the trait is simple. When the trait is determined by few loci, they are reminiscent of classical experimental designs for regression models and tend to select homozygous individuals. When the trait is determined by many loci, locus effects may be difficult to estimate, even if an optimized design is used.
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Affiliation(s)
- Olivier David
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, Évolution, Génomes, Comportement, Écologie, 91198, Gif-sur-Yvette, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
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Vidal T, Aissaoui H, Rehali S, Andrieu B. Two maize cultivars of contrasting leaf size show different leaf elongation rates with identical patterns of extension dynamics and coordination. AOB PLANTS 2021; 13:plaa072. [PMID: 33604014 PMCID: PMC7877697 DOI: 10.1093/aobpla/plaa072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 06/09/2023]
Abstract
Simulating leaf development from initiation to maturity opens new possibilities to model plant-environment interactions and the plasticity of plant architecture. This study analyses the dynamics of leaf production and extension along a maize (Zea mays) shoot to assess important modelling choices. Maize plants from two cultivars originating from the same inbred line, yet differing in the length of mature leaves were used in this study. We characterized the dynamics of the blade and sheath lengths of all phytomers by dissecting plants every 2-3 days. We analysed how differences in leaf size were built up and we examined the coordination between the emergence of organs and phases of their extension. Leaf extension rates were higher in the cultivar with longer leaves than in the cultivar with shorter leaves; no differences were found in other aspects. We found that (i) first post-embryonic leaves were initiated at a markedly higher rate than upper leaves; (ii) below ear position, sheaths were initiated at a time intermediate between tip emergence and appearance, while above the ear position, sheaths were initiated at a high rate, such that the time interval between the blade and sheath initiations decreased for these leaves; and (iii) ear position also marked a change in the correlation in size between successive phytomers with little correlation of size between upper and lower leaves. Our results identified leaf extension rate as the reason for the difference in size between the two cultivars. The two cultivars shared the same pattern for the timing of initiation events, which was more complex than previously thought. The differences described here may explain some inaccuracies reported in functional-structural plant models. We speculate that genotypic variation in behaviour for leaf and sheath initiation exists, which has been little documented in former studies.
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Affiliation(s)
- Tiphaine Vidal
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Hafssa Aissaoui
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Sabrina Rehali
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Bruno Andrieu
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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Abstract
Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize-the teosintes Zea mays ssp. parviglumis and ssp. mexicana-as excellent models for dissecting long-term local adaptation.Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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Durand E, Tenaillon MI, Raffoux X, Thépot S, Falque M, Jamin P, Bourgais A, Ressayre A, Dillmann C. Dearth of polymorphism associated with a sustained response to selection for flowering time in maize. BMC Evol Biol 2015; 15:103. [PMID: 26049736 PMCID: PMC4458035 DOI: 10.1186/s12862-015-0382-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/18/2015] [Indexed: 12/25/2022] Open
Abstract
Background Long term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines. Results Our experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs’ pedigrees results in strong genetic differentiation between populations and families. Conclusions Our results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0382-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eleonore Durand
- INRA, Ferme du Moulon, Gif sur Yvette, 91190, France. .,CNRS, Ferme du Moulon, Gif sur Yvette, 91190, France.
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11
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Smadi C. An eco-evolutionary approach of adaptation and recombination in a large population of varying size. Stoch Process Their Appl 2015. [DOI: 10.1016/j.spa.2014.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:51-9. [PMID: 24631844 DOI: 10.1016/j.pbi.2014.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/04/2014] [Accepted: 02/09/2014] [Indexed: 05/25/2023]
Abstract
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
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Affiliation(s)
- Paul Gepts
- University of California, Department of Plant Sciences/MS 1, Section of Crop and Ecosystem Sciences, 1 Shields Avenue, Davis, CA 95616, United States of America.
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Startek M, Le Rouzic A, Capy P, Grzebelus D, Gambin A. Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations. Theor Popul Biol 2013; 90:145-51. [PMID: 23948701 DOI: 10.1016/j.tpb.2013.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 11/17/2022]
Abstract
Transposable elements are DNA segments capable of persisting in host genomes by self-replication in spite of deleterious mutagenic effects. The theoretical dynamics of these elements within genomes has been studied extensively, and population genetic models predict that they can invade and maintain as a result of both intra-genomic and inter-individual selection in sexual species. In asexuals, the success of selfish DNA is more difficult to explain. However, most theoretical work assumes constant environment. Here, we analyze the impact of environmental change on the dynamics of transposition activity when horizontal DNA exchange is absent, based on a stochastic computational model of transposable element proliferation. We argue that repeated changes in the phenotypic optimum in a multidimensional fitness landscape may induce explosive bursts of transposition activity associated with faster adaptation. However, long-term maintenance of transposition activity is unlikely. This could contribute to the significant variation in the transposable element copy number among closely related species.
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Affiliation(s)
- Michał Startek
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Poland
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14
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Abstract
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to adaptation when co-opted--e.g., following a mutation increasing expression from a low, attenuated baseline. This view is described, for example, by the metaphor of the spread of a population across a neutral network in genotype space. As an alternative view, consider the fact that most phenotypic traits are affected by multiple sequences, including cryptic ones. Even in a strictly clonal population, the co-option of cryptic sequences at different loci may have different phenotypic effects and offer the population multiple adaptive possibilities. Here, we model the evolution of quantitative phenotypic characters encoded by cryptic sequences and compare the relative contributions of genetic diversity and of variation across sites to the phenotypic potential of a population. We show that most of the phenotypic variation accessible through co-option would exist even in populations with no polymorphism. This is made possible by a history of compensatory evolution, whereby the phenotypic effect of a cryptic mutation at one site was balanced by mutations elsewhere in the genome, leading to a diversity of cryptic effect sizes across sites rather than across individuals. Cryptic sequences might accelerate adaptation and facilitate large phenotypic changes even in the absence of genetic diversity, as traditionally defined in terms of alternative alleles.
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Glémin S, Ronfort J. Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation. Evolution 2012; 67:225-40. [PMID: 23289574 DOI: 10.1111/j.1558-5646.2012.01778.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Evolution of selfing from outcrossing recurrently occurred in many lineages, especially in flowering plants. Evolution of selfing induces dramatic changes in the population genetics functioning but its consequences on the dynamics of adaptation have been overlooked. We studied a simple one-locus model of adaptation where a population experiences an environmental change at a given time. We first determined the effect of the mating system on the genetic bases and the speed of adaptation, focusing on the dominance of beneficial mutations and the respective part of standing variation and new mutations. Then, we assumed that the environmental change is associated with population decline to determine the effect of the mating system on the probability of population extinction. Extending previous results, we found that adaptation is more efficient and extinction less likely in outcrossers when beneficial mutations are dominant and codominant and when standing variation plays a significant role in adaptation. However, given adaptation does occur, it is usually more rapid in selfers than in outcrossers. Our results bear implications for the evolution of the selfing syndrome, the dynamics of the domestication process, and the dead-end hypothesis that posits that selfing lineages are doomed to extinction on the long run.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 CNRS, Place Eugéne Bataillon, 34095 Montpellier cedex 5, France.
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Abstract
In a previous study, we identified a candidate fragment length polymorphism associated with flowering time variation after seven generations of selection for flowering time, starting from the maize inbred line F252. Here, we characterized the candidate region and identified underlying polymorphisms. Then, we combined QTL mapping, association mapping, and developmental characterization to dissect the genetic mechanisms responsible for the phenotypic variation. The candidate region contained the Eukaryotic Initiation Factor (eIF-4A) and revealed a high level of sequence and structural variation beyond the 3'-UTR of eIF-4A, including several insertions of truncated transposable elements. Using a biallelic single-nucleotide polymorphism (SNP) (C/T) in the candidate region, we confirmed its association with flowering time variation in a panel of 317 maize inbred lines. However, while the T allele was correlated with late flowering time within the F252 genetic background, it was correlated with early flowering time in the association panel with pervasive interactions between allelic variation and the genetic background, pointing to underlying epistasis. We also detected pleiotropic effects of the candidate polymorphism on various traits including flowering time, plant height, and leaf number. Finally, we were able to break down the correlation between flowering time and leaf number in the progeny of a heterozygote (C/T) within the F252 background consistent with causal loci in linkage disequilibrium. We therefore propose that both a cluster of tightly linked genes and epistasis contribute to the phenotypic variation for flowering time.
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Population genetics of genomics-based crop improvement methods. Trends Genet 2011; 27:98-106. [PMID: 21227531 DOI: 10.1016/j.tig.2010.12.003] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/09/2010] [Accepted: 12/09/2010] [Indexed: 01/24/2023]
Abstract
Many genome-wide association studies (GWAS) in humans are concluding that, even with very large sample sizes and high marker densities, most of the genetic basis of complex traits may remain unexplained. At the same time, recent research in plant GWAS is showing much greater success with fewer resources. Both GWAS and genomic selection (GS), a method for predicting phenotypes by the use of genome-wide marker data, are receiving considerable attention among plant breeders. In this review we explore how differences in population genetic histories, as well as past selection for traits of interest, have produced trait architectures and patterns of linkage disequilibrium (LD) that frequently differ dramatically between domesticated plants and humans, making detection of quantitative trait loci (QTL) effects in crops more rewarding and less costly than in humans.
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Salvi S, Corneti S, Bellotti M, Carraro N, Sanguineti MC, Castelletti S, Tuberosa R. Genetic dissection of maize phenology using an intraspecific introgression library. BMC PLANT BIOLOGY 2011; 11:4. [PMID: 21211047 PMCID: PMC3025946 DOI: 10.1186/1471-2229-11-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 01/06/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Collections of nearly isogenic lines where each line carries a delimited portion of a donor source genome into a common recipient genetic background are known as introgression libraries and have already shown to be instrumental for the dissection of quantitative traits. By means of marker-assisted backcrossing, we have produced an introgression library using the extremely early-flowering maize (Zea mays L.) variety Gaspé Flint and the elite line B73 as donor and recipient genotypes, respectively, and utilized this collection to investigate the genetic basis of flowering time and related traits of adaptive and agronomic importance in maize. RESULTS The collection includes 75 lines with an average Gaspé Flint introgression length of 43.1 cM. The collection was evaluated for flowering time, internode length, number of ears, number of nodes (phytomeres), number of nodes above the ear, number and proportion of nodes below the ear and plant height. Five QTLs for flowering time were mapped, all corresponding to major QTLs for number of nodes. Three additional QTLs for number of nodes were mapped. Besides flowering time, the QTLs for number of nodes drove phenotypic variation for plant height and number of nodes below and above the top ear, but not for internode length. A number of apparently Mendelian-inherited phenotypes were also observed. CONCLUSIONS While the inheritance of flowering time was dominated by the well-known QTL Vgt1, a number of other important flowering time QTLs were identified and, thanks to the type of plant material here utilized, immediately isogenized and made available for fine mapping. At each flowering time QTL, early flowering correlated with fewer vegetative phytomeres, indicating the latter as a key developmental strategy to adapt the maize crop from the original tropical environment to the northern border of the temperate zone (southern Canada), where Gaspé Flint was originally cultivated. Because of the trait differences between the two parental genotypes, this collection will serve as a permanent source of nearly isogenic materials for multiple studies of QTL analysis and cloning.
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Affiliation(s)
- Silvio Salvi
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Simona Corneti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Massimo Bellotti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Nicola Carraro
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
- Department of Horticulture and Landscape Architecture, 625 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, USA
| | - Maria C Sanguineti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Sara Castelletti
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
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