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Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thaliana
Ilkka Kronholm, Olivier Loudet, Juliette de Meaux
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-33
Abstract: If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only ΦST, an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of ΦST depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that QST has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology.We find that alternative measures of differentiation like F'ST and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as ΦST. Furthermore, in systems where migration between populations is low, such as A. thaliana, QST < FST cannot be taken as evidence for homogenising selection as has been traditionally thought.Characterisation of population structure is a pivotal task in population genetics. It is important for inferring the evolutionary history of a species, assisting in conservation studies [1] and measuring dispersal [2-4]. In association mapping and forensic applications, population structure must be corrected for [see [5]]. The characterisation of population structure is also crucial for studies tracking the signature of local adaptation i. e. when natural selection maintains differences in allele frequencies between populations. Indeed, limited migration or population bottlenecks can also cause allele frequencies to diverge. A proper characterisation of population structure is absolutely required to infer the action of local selection on outlier loci with
Correction: Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thaliana
Ilkka Kronholm, Olivier Loudet, Juliette de Meaux
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-88
Abstract: In the introduction of Kronholm et al. [1], we discuss what properties a differentiation measure, like FST, should or was assumed to have. Recent developments [2-5] have shown that FST in fact does not have these properties. Our intention was to take a chronological approach, referring to FST as it has traditionally been referred to and subsequently emphasizing some of the problems this measure has.Genetic differentiation among populations, that is differences in allele frequencies, is caused by multiple factors, demographic factors (genetic drift, migration etc.) and mutations.Our goal was to identify which measure should be used when only the demographic parameters are of interest. This is the case when genetic divergence is examined in order to detect local adaptation and assess the ecological relevance of natural variation. In this case ΦST can be useful, if different markers need to be compared to each other. Given this context, this is why we state that the measure should be independent of mutation rate.On the other hand, if one is interested in the question: is there genetic differentiation per se among the studied populations? Then, a measure like D should be used because it measures the absolute genetic differentiation present. We do not wish to advocate in general that a measure of genetic differentiation should be independent of mutation rate.In some places of our paper this message does not come through clearly, because our phrasing may be less than ideal. Also, sometimes the word "estimator" was used when "measure" would have been a better choice. We do not wish to say for example that D is a "statistical estimator" of FST but that these are different measures of genetic divergence.Furthermore, we wish to address table 1, where the expected value of FST, and values for D and F'ST are given in the same table. Here, it was not stated clearly enough that values of D and F'ST cannot be directly compared to the expected FST value. The idea here was to show h
Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana
Daniela Vlad,Fabrice Rappaport,Matthieu Simon,Olivier Loudet
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1000945
Abstract: A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale.
Natural Variation in Partial Resistance to Pseudomonas syringae Is Controlled by Two Major QTLs in Arabidopsis thaliana
Laure Perchepied, Thomas Kroj, Maurice Tronchet, Olivier Loudet, Dominique Roby
PLOS ONE , 2006, DOI: 10.1371/journal.pone.0000123
Abstract: Background Low-level, partial resistance is pre-eminent in natural populations, however, the mechanisms underlying this form of resistance are still poorly understood. Methodology/Principal Findings In the present study, we used the model pathosystem Pseudomonas syringae pv. tomato DC3000 (Pst) - Arabidopsis thaliana to study the genetic basis of this form of resistance. Phenotypic analysis of a set of Arabidopsis accessions, based on evaluation of in planta pathogen growth revealed extensive quantitative variation for partial resistance to Pst. It allowed choosing a recombinant inbred line (RIL) population derived from a cross between the accessions Bayreuth and Shahdara for quantitative genetic analysis. Experiments performed under two different environmental conditions led to the detection of two major and two minor quantitative trait loci (QTLs) governing partial resistance to Pst and called PRP-Ps1 to PRP-Ps4. The two major QTLs, PRP-Ps1 and PRP-Ps2, were confirmed in near isogenic lines (NILs), following the heterogeneous inbred families (HIFs) strategy. Analysis of marker gene expression using these HIFs indicated a negative correlation between the induced amount of transcripts of SA-dependent genes PR1, ICS and PR5, and the in planta bacterial growth in the HIF segregating at PRP-Ps2 locus, suggesting an implication of PRP-Ps2 in the activation of SA dependent responses. Conclusions/Significance These results show that variation in partial resistance to Pst in Arabidopsis is governed by relatively few loci, and the validation of two major loci opens the way for their fine mapping and their cloning, which will improve our understanding of the molecular mechanisms underlying partial resistance.
Allelic Heterogeneity and Trade-Off Shape Natural Variation for Response to Soil Micronutrient
Seifollah Poormohammad Kiani,Charlotte Trontin,Matthew Andreatta,Matthieu Simon,Thierry Robert,David E. Salt,Olivier Loudet
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002814
Abstract: As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness.
Natural Variation in Seed Very Long Chain Fatty Acid Content Is Controlled by a New Isoform of KCS18 in Arabidopsis thaliana
Sophie Jasinski, Alain Lécureuil, Martine Miquel, Olivier Loudet, Sylvain Raffaele, Marine Froissard, Philippe Guerche
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049261
Abstract: Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR.2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the β-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR.2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants.
Disentangling the Intertwined Genetic Bases of Root and Shoot Growth in Arabidopsis
Marie Bouteillé, Ga?lle Rolland, Crispulo Balsera, Olivier Loudet, Bertrand Muller
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032319
Abstract: Root growth and architecture are major components of plant nutrient and water use efficiencies and these traits are the matter of extensive genetic analysis in several crop species. Because root growth relies on exported assimilate from the shoot, and changes in assimilate supply are known to alter root architecture, we hypothesized (i) that the genetic bases of root growth could be intertwined with the genetic bases of shoot growth and (ii) that the link could be either positive, with alleles favouring shoot growth also favouring root growth, or negative, because of competition for assimilates. We tested these hypotheses using a quantitative genetics approach in the model species Arabidopsis thaliana and the Bay-0×Shahdara recombinant inbred lines population. In accordance with our hypothesis, root and shoot growth traits were strongly correlated and most root growth quantitative trait loci (QTLs) colocalized with shoot growth QTLs with positive alleles originating from either the same or the opposite parent. In order to identify regions that could be responsible for root growth independently of the shoot, we generated new variables either based on root to shoot ratios, residuals of root to shoot correlations or coordinates of principal component analysis. These variables showed high heritability allowing genetic analysis. They essentially all yielded similar results pointing towards two regions involved in the root – shoot balance. Using Heterogeneous Inbred Families (a kind of near-isogenic lines), we validated part of the QTLs present in these two regions for different traits. Our study thus highlights the difficulty of disentangling intertwined genetic bases of root and shoot growth and shows that this difficulty can be overcome by using simple statistical tools.
Dispersions of ellipsoidal particles in a nematic liquid crystal
Mykola Tasinkevych,Frederic Mondiot,Olivier Mondain-Monval,Jean-Christophe Loudet
Physics , 2013,
Abstract: Colloidal particles dispersed in a partially ordered medium, such as a liquid crystal (LC) phase, disturb its alignment and are subject to elastic forces. These forces are long-ranged, anisotropic and tunable through temperature or external fields, making them a valuable asset to control colloidal assembly. The latter is very sensitive to the particle geometry since it alters the interactions between the colloids. We here present a detailed numerical analysis of the energetics of elongated objects, namely prolate ellipsoids, immersed in a nematic host. The results, complemented with qualitative experiments, reveal novel LC configurations with peculiar topological properties around the ellipsoids, depending on their aspect ratio and the boundary conditions imposed on the nematic order parameter. The latter also determine the preferred orientation of ellipsoids in the nematic field, because of elastic torques, as well as the morphology of particles aggregates.
Identification of QTLs controlling gene expression networks defined a priori
Daniel J Kliebenstein, Marilyn AL West, Hans van Leeuwen, Olivier Loudet, RW Doerge, Dina A St Clair
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-308
Abstract: We describe a statistical approach that is capable of assessing higher-order a priori defined gene network response, as measured by microarrays. This analysis detected significant network variation between two Arabidopsis thaliana accessions, Bay-0 and Shahdara. By extending this approach, we were able to identify eQTLs controlling network responses for 18 out of 20 a priori-defined gene networks in a recombinant inbred line population derived from accessions Bay-0 and Shahdara.This approach has the potential to be expanded to facilitate direct tests of the relationship between phenotypic trait and transcript genetic architecture. The use of a priori definitions for network eQTL identification has enormous potential for providing direction toward future eQTL analyses.Many phenotypic traits, ranging from disease susceptibility to development, are quantitative in nature and are studied in both animals and plants via quantitative trait locus (QTL) mapping [1-3]. QTLs are regions of the genome associated with phenotypic variation for a trait. These regions may or may not contain genes that, when differentially expressed, control the associated phenotypic variation. One approach that explores the relationship of phenotypic trait variation with transcriptome variation employs microarrays to survey global gene expression across a sample of individuals from a segregating population, and then maps expression QTLs (eQTLs) [4-7]. An inventory of eQTLs representing a population or species may provide the necessary information required for identifying genes that control quantitative phenotypes. Categorizing eQTLs has the potential to enable reverse (natural variation) genetics approaches for the identification of genes controlling quantitative traits, and may also help to enhance the rate of QTL cloning [8].Global eQTL analyses also allow evolutionary biologists and geneticists a broader view of molecular complexities. For example, what is the level of cis versus trans polymorph
Extensive Natural Epigenetic Variation at a De Novo Originated Gene
Amanda Bortolini Silveira,Charlotte Trontin,Sandra Cortijo,Joan Barau,Luiz Eduardo Vieira Del Bem,Olivier Loudet,Vincent Colot ,Michel Vincentz
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003437
Abstract: Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
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