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1.
New Phytol ; 2019 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-31711257

RESUMO

Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so-called 'exapted' resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host-pathogen compatibility was assessed by recording infection success and pathogen growth in a full-sib family of Quercus robur under controlled and natural conditions. Two high-resolution genetic maps anchored on the reference genome were used to study the genetic architecture of resistance and to identify positional candidate genes. Two genomic regions, each containing six strong and stable quantitative trait loci (QTLs) accounting for 12-19% of the phenotypic variation, were mainly associated with E. alphitoides infection. Candidate genes, especially genes encoding receptor-like-kinases and galactinol synthases, were identified in these regions. The three QTLs associated with P. cinnamomi infection did not colocate with QTLs found for E. alphitoides. These findings provide evidence that exapted resistance to E. alphitoides and P. cinnamomi is present in Q. robur and suggest that the underlying molecular mechanisms involve genes encoding proteins with extracellular signaling functions.

2.
Nat Commun ; 10(1): 5230, 2019 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-31745089

RESUMO

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.

3.
Tree Physiol ; 39(4): 615-627, 2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30668790

RESUMO

Research on plant-herbivore interactions has long recognized that plant genetic variation plays a central role in driving insect abundance and herbivory, as well as in determining plant defense. However, how plant genes influence herbivore feeding performances, and which plant defensive traits mediate these effects, remain poorly understood. Here we investigated the feeding performances of two insect leaf chewers with contrasting diet breadth (the generalist Lymantria dispar L. and the specialist Thaumetopoea processionea L.) on different genotypes of pedunculate oak (Quercus robur L.) and tested the role of leaf phenolics. We used leaves from four clones of 30 Q. robur full-sibs grown in a common garden to estimate the performance of both herbivores in laboratory feeding trials and to quantify the concentration of constitutive chemical defences (phenolic compounds). We found that tree genetics influenced leaf consumption by T. processionea but not by L. dispar. However genetic variation among trees did not explain growth rate variation in either herbivore nor in leaf phenolics. Interestingly, all phenolic compounds displayed a positive relationship with L. dispar growth rate, and leaf consumption by both herbivores displayed a positive relationship with the concentrations of condensed tannins, suggesting that highly defended leaves could induce a compensatory feeding response. While genetic variation in oaks did not explain herbivore growth rate, we found positive genetic correlations between the two herbivores for leaf consumption and digestion. Overall, we found that oak genotype and phenolic compounds partly and independently contribute to variability in herbivore performance. We challenged the current view of plant-insect interaction and provided little support to the idea that the effect of plant genotype on associated organisms is driven by plant defences. Together, our results point to the existence of genetically determined resistance traits in oaks whose effects differ between herbivores and motivate further research on mechanisms governing oak-herbivore interactions.


Assuntos
Variação Genética , Interações Hospedeiro-Parasita , Hidroxibenzoatos/metabolismo , Mariposas/fisiologia , Doenças das Plantas/imunologia , Quercus/fisiologia , Animais , Genótipo , Herbivoria , Fenótipo , Doenças das Plantas/parasitologia , Folhas de Planta/química , Folhas de Planta/imunologia , Folhas de Planta/fisiologia , Quercus/química , Quercus/imunologia
4.
Plant J ; 97(1): 164-181, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30466152

RESUMO

Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe-related traits were developed in the relatively simple context of binary host-microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome-wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant-microbe interactions will influence the choice of traits to be mapped.


Assuntos
Estudo de Associação Genômica Ampla , Interações entre Hospedeiro e Microrganismos , Microbiota , Plantas/genética , Plantas/microbiologia
5.
Nat Plants ; 4(7): 440-452, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29915331

RESUMO

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.


Assuntos
Genoma de Planta/genética , Quercus/genética , Evolução Biológica , DNA de Plantas/genética , Variação Genética/genética , Longevidade/genética , Mutação , Filogenia , Análise de Sequência de DNA
6.
PLoS Genet ; 14(2): e1007155, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29432421

RESUMO

By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by "natural evolution experiments" that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.


Assuntos
Genoma de Planta , Taxa de Mutação , Mutação/fisiologia , Desenvolvimento Vegetal/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Cruzamentos Genéticos , Evolução Molecular Direcionada , Evolução Molecular , Fluxo Gênico/fisiologia , Espécies Introduzidas , Fenótipo , Filogenia , Plantas Daninhas/genética , Plantas Daninhas/crescimento & desenvolvimento , Seleção Genética , Análise de Sequência de DNA
7.
Proc Natl Acad Sci U S A ; 112(13): 4032-7, 2015 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-25775585

RESUMO

The "mustard oil bomb" is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genome-wide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide [Formula: see text] scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe.


Assuntos
Arabidopsis/química , Glucosinolatos/química , Herbivoria , Seleção Genética , Alelos , Animais , Arabidopsis/genética , Biodiversidade , Cromatografia Líquida , Epistasia Genética , Evolução Molecular , Genômica , Genótipo , Geografia , Insetos , Desequilíbrio de Ligação , Metionina/química , Polimorfismo de Nucleotídeo Único , Análise de Componente Principal , Locos de Características Quantitativas , Espectrometria de Massas em Tandem
8.
Mol Ecol ; 22(16): 4222-4240, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23875782

RESUMO

Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into the spatial scale of adaptive variation by identifying the putative selective agents responsible for this selection. Forty-nine natural stands from four climatically contrasted French regions were characterized (i) phenologically for six traits, (ii) genetically using 135 SNP markers and (iii) ecologically for 42 variables. Up to 63% of phenological variation could be explained by neutral genetic diversity. The remaining phenological variation displayed stronger associations with ecological variation within regions than among regions, suggesting the importance of local selective agents in shaping adaptive phenological variation. Although climatic conditions have often been suggested as the main selective agents acting on phenology in A. thaliana, both edaphic conditions and interspecific competition appear to be strong selective agents in some regions. In a first attempt to identify the genetics of phenological variation at different geographical scales, we phenotyped worldwide accessions and local polymorphic populations from the French RegMap in a genome-wide association (GWA) mapping study. The genomic regions associated with phenological variation depended upon the geographical scale considered, stressing the need to account for the scale of adaptive phenotypic variation when choosing accession panels for GWAS.


Assuntos
Adaptação Fisiológica/genética , Arabidopsis , Clima , Ecossistema , Variação Genética , Seleção Genética , Adaptação Fisiológica/fisiologia , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Mapeamento Cromossômico , Flores/genética , Flores/crescimento & desenvolvimento , Genética Populacional , Genoma de Planta , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único
9.
Acta Bot Gallica ; 160(3-4): 205-219, 2013 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-24470785

RESUMO

Often used as a proxy for the transition to reproduction, flowering time (FT) is an integrative trait of two successive biological processes, i.e. bolting time (BT) and the interval between bolting and flowering time (INT). In this study, we aimed to identify candidate genes associated with these composite traits in Arabidopsis thaliana using a field experiment. Genome-wide association (GWA) mapping was performed on BT, INT and FT based on a sample of 179 worldwide natural accessions genotyped for 216,509 SNPs. The high resolution conferred by GWA mapping indicates that FT is an integrative trait at the genetic level, with distinct genetics for BT and INT. BT is shaped largely by genes involved in the circadian clock whereas INT is shaped by genes involved in both the hormone pathways and cold acclimation. Finally, the florigen TSF appears to be the main integrator of environmental and internal signals in ecologically realistic conditions. Based on FT scored in a previous field experiment, we also studied the genetics underlying reaction norms across two years. Only four genes were common to both years, emphasizing the need to repeat field experiments. The gene regulation model appeared as the main genetic model for genotype × year interactions.

10.
PLoS One ; 7(3): e32069, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22403624

RESUMO

Phenological traits often show variation within and among natural populations of annual plants. Nevertheless, the adaptive value of post-anthesis traits is seldom tested. In this study, we estimated the adaptive values of pre- and post-anthesis traits in two stressful environments (water stress and interspecific competition), using the selfing annual species Arabidopsis thaliana. By estimating seed production and by performing laboratory natural selection (LNS), we assessed the strength and nature (directional, disruptive and stabilizing) of selection acting on phenological traits in A. thaliana under the two tested stress conditions, each with four intensities. Both the type of stress and its intensity affected the strength and nature of selection, as did genetic constraints among phenological traits. Under water stress, both experimental approaches demonstrated directional selection for a shorter life cycle, although bolting time imposes a genetic constraint on the length of the interval between bolting and anthesis. Under interspecific competition, results from the two experimental approaches showed discrepancies. Estimation of seed production predicted directional selection toward early pre-anthesis traits and long post-anthesis periods. In contrast, the LNS approach suggested neutrality for all phenological traits. This study opens questions on adaptation in complex natural environment where many selective pressures act simultaneously.


Assuntos
Adaptação Fisiológica/genética , Evolução Molecular Direcionada/métodos , Meio Ambiente , Laboratórios , Periodicidade , Sementes/crescimento & desenvolvimento , Estresse Fisiológico/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Flores/genética , Flores/crescimento & desenvolvimento , Flores/fisiologia , Genótipo , Fenótipo , Sementes/genética , Sementes/fisiologia
11.
Genome Biol ; 12(10): 232, 2011 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-22035733

RESUMO

Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.


Assuntos
Arabidopsis/genética , Estudos de Associação Genética , Padrões de Herança , Oryza/genética , Polimorfismo de Nucleotídeo Único , Zea mays/genética , Adaptação Biológica , Alelos , Arabidopsis/fisiologia , Mapeamento Cromossômico , Genes de Plantas , Genótipo , Oryza/fisiologia , Fenótipo , Seleção Genética , Zea mays/fisiologia
12.
Science ; 334(6052): 83-6, 2011 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-21980108

RESUMO

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.


Assuntos
Aclimatação/genética , Arabidopsis/genética , Arabidopsis/fisiologia , Clima , Aptidão Genética , Genoma de Planta , Polimorfismo de Nucleotídeo Único , Seleção Genética , Adaptação Fisiológica/genética , Alelos , Arabidopsis/crescimento & desenvolvimento , Ásia , Mudança Climática , Metabolismo Energético , Europa (Continente) , Pleiotropia Genética , Estudo de Associação Genômica Ampla , Desequilíbrio de Ligação , Temperatura Ambiente , Água
13.
PLoS Genet ; 6(5): e1000940, 2010 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-20463887

RESUMO

Flowering time is a key life-history trait in the plant life cycle. Most studies to unravel the genetics of flowering time in Arabidopsis thaliana have been performed under greenhouse conditions. Here, we describe a study about the genetics of flowering time that differs from previous studies in two important ways: first, we measure flowering time in a more complex and ecologically realistic environment; and, second, we combine the advantages of genome-wide association (GWA) and traditional linkage (QTL) mapping. Our experiments involved phenotyping nearly 20,000 plants over 2 winters under field conditions, including 184 worldwide natural accessions genotyped for 216,509 SNPs and 4,366 RILs derived from 13 independent crosses chosen to maximize genetic and phenotypic diversity. Based on a photothermal time model, the flowering time variation scored in our field experiment was poorly correlated with the flowering time variation previously obtained under greenhouse conditions, reinforcing previous demonstrations of the importance of genotype by environment interactions in A. thaliana and the need to study adaptive variation under natural conditions. The use of 4,366 RILs provides great power for dissecting the genetic architecture of flowering time in A. thaliana under our specific field conditions. We describe more than 60 additive QTLs, all with relatively small to medium effects and organized in 5 major clusters. We show that QTL mapping increases our power to distinguish true from false associations in GWA mapping. QTL mapping also permits the identification of false negatives, that is, causative SNPs that are lost when applying GWA methods that control for population structure. Major genes underpinning flowering time in the greenhouse were not associated with flowering time in this study. Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes.


Assuntos
Arabidopsis/crescimento & desenvolvimento , Arabidopsis/genética , Ligação Genética , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Proteínas de Arabidopsis/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Flores/genética , Flores/crescimento & desenvolvimento , Dados de Sequência Molecular , Locos de Características Quantitativas , Estações do Ano
14.
Nature ; 465(7298): 627-31, 2010 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-20336072

RESUMO

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.


Assuntos
Arabidopsis/classificação , Arabidopsis/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Fenótipo , Alelos , Proteínas de Arabidopsis/genética , Flores/genética , Genes de Plantas/genética , Loci Gênicos/genética , Genótipo , Imunidade Inata/genética , Endogamia , Polimorfismo de Nucleotídeo Único/genética
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