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Introduction
My main interest is in the quantitative genetics of Genotype x Environment interactions in model plants
Additional affiliations
May 2002 - May 2004
June 1998 - April 2002
December 1996 - May 1998
Publications
Publications (132)
Energy production and metabolism are intimately linked to ecological and environmental constraints across the tree of life. In plants, which depend on sunlight to produce energy, the link between primary metabolism and the environment is especially strong. By governing CO2 uptake for photosynthesis and transpiration, leaf pores, or stomata, couple...
Background
How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leverage publicly available multi-omic and bio-climatic data for more than 1000 wild Arabidopsis thaliana accessions to determine the...
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosse...
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosse...
Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to their environment. Applying classical quantitative genetics on a segregating population derived from a Can-0xCol-0 cross, we identify the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a...
Whether environmentally-induced changes in phenotypes can be heritable is a topic with revived interest. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown if this other system of inheritance responds to environmental changes and if it ca...
Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to the environment. We used leaf growth as a model trait as it is highly integrative of internal and external cues and relies on functions at different levels of the plant organization. Applying class...
One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architec-tures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment...
Distributions of the mean phenotypic values across RILs.
Frequency histograms showing the distributions of the PRA29, RER16-29 and Compactness29 traits within each of the four RIL sets in well-watered (WW: blue) and water deficit (WD: orange) conditions. Phenotypic values for parental accessions from these specific experiments are indicated by blue...
Dissection of a genomic region in CvixCol for RER16-29 and Compactness29 ('microStairs' approach).
Same legend as Fig 7.
(PDF)
microStairs; genotypic description of recombinant lines.
The genotypes of the 31 lines selected for the microStairs experiment are indicated along this 3Mb region of the top of chromosome 1 with markers localized on the physical map (kb).
(PDF)
microStairs; differentially expressed genes controlled in cis.
List of Cvi/Col differentially expressed genes in an allele-specific fashion ([log2]>0.8 in at least one condition; from Cubillos et al., 2014) across the whole region.
(PDF)
Distribution of QTL effects.
Distribution of the QTL effects (R2%) in the four RILs populations (CvixCol, BurxCol, BlaxCol, YoxCol), two conditions (WW and WD) and for the 3 traits considered in the analysis (PRA29, RER16-29, Compactness29).
(PDF)
Heritabilities of the observed phenotypes.
Broad-sense heritabilities (h2) in the 4 RIL sets (BlaxCol, CvixCol, BurxCol and YoxCol) for PRA29, RER16-29 and Compactness29 in WW and WD conditions. H2 > 0.4 are highlighted in bold. Broad-sense heritabilities were calculated with the following equation h2 = Var(G)/Var(P) with Var(P) = Var(G)+Var(E)
(PD...
Multi-cross QTL analysis for RER16-29.
Same legend as Fig 5. Chromosome 3 shows no significant combined QTLs for RER16-29.
(PDF)
Multi-cross QTL analysis for Compactness29.
Same legend as Fig 5.
(PDF)
Near isogenic lines-based validation of QTLs for RER16-29 and Compactness29.
Same legend as Fig 6.
(PDF)
microStairs; polymorphisms segregating in different bins.
This table lists all known polymorphisms between Col-0 and Cvi-0 that can potentially affect gene function (according to 1001Genomes data) within PRA29-significant bins only: in the selected physical interval, genes with more than 3 non-synonymous SNP or a high-impact polymorphism are highli...
2D scans for epistasis.
Heatmaps representing the LOD score of the interaction effects between all pairs of loci for 4 RIL sets, 3 traits, in 2 conditions. Each heatmap shows the pairwise interaction effects obtained in control condition WW (triangle above diagonal) and in water deficit condition WD (triangle below diagonal). The color scale (LOD s...
Analyses of variance for genotype, experiment and condition factors, and their interactions.
For each RIL set, -log(p values) of main and interaction effects calculated by the analysis of variance (ANOVA) from the following model:
Yijkl~μ+αi+βj+γk+δij+λjk+σik+εijkl.
where Yijkl: phenotype; μ: mean; αi: effect of the condition; βj: effect of the exp...
Mapped QTL parameters across RIL sets, traits and conditions.
For each RIL set, trait and condition (or GxE interaction term: 'inter'): every independent QTL peak is a row in the table, indicating its localisation (chromosome and position on the genetic map), its significance (maximum LOD score) and its effect (direction of the allelic effect: 'sig...
Soil water uptake by roots is a key component of plant performance and adaptation to adverse environments. Here, we use a genome-wide association analysis to identify the XYLEM NAC DOMAIN 1 (XND1) transcription factor as a negative regulator of Arabidopsis root hydraulic conductivity (Lpr). The distinct functionalities of a series of natural XND1 v...
Whether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are...
One of the main outcome of quantitative genetic approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or...
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computin...
While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, whil...
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolu- tion, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has...
A promising method for characterizing the phenotype of a plant as an interaction between its genotype and its environment is to use refined organ-scale plant growth models that use the observation of architectural traits, such as leaf area, containing a lot of information on the whole history of the functioning of the plant. The Phenoscope, a high-...
PCR#2 and PCR#3 are specific to chromosome 5.
PCR#2 and PCR#3 amplicons are positioned in Fig 2A. The reverse primer for PCR#2 and the forward primer for PCR#3 are overlapping a short deletion of 7 bp between chromosomes 1 and 5 (S1 Text). (A) PCR amplification on genomic DNAs extracted from plants with the indicated genotypes. K1NokK5Col correspon...
TAD3-1 is expressed differently in Nok-1 and Col-0.
Expression analysis of the TAD3-1 copy in both Nok-1 and Col-0. The region amplified corresponds to PCR#3 (Fig 2A) and is specific for TAD3-1 (S4 Fig). The numbers of cycles are indicated, and Col-0 genomic DNA was used as control. ATEF amplifications served as controls.
(PDF)
TAD3-1 expression analysis using pyrosequencing.
(A) Dispensation order used to analyze the A/T SNP. (B) Pyrograms obtained for the control DNAs. The luminescence is expressed in arbitrary unit (a.u.). Along the abscissa the dispensation order is given with controls (E: enzyme; S: substrate). The SNP position is tinted in grey with the calculated p...
Distribution of small RNA reads over the TAD3-1 locus.
sRNA content of the region corresponding to the mapping interval (Chr5: 8,440,101–8,453,801). sRNAs from Col-0, Nok-1 and the Col-0xNok-1 F1 were mapped to the Col-0 genome (TAIR10.30 version). Both sense and antisense reads were collapsed and only reads corresponding to 21 to 24-nt are plotted...
Scheme showing crosses done to obtain the TAD3 loci in different mutant backgrounds.
Example of cross between Nok-1 and a mutant (here nrpe1-11) in a Col-0 background performed to obtain a plant fixed for the mutation and heterozygous at both TAD3 loci.
(PDF)
Methylation patterns of the promoter regions in incompatible plants carrying a cmt3-11 mutation.
After bisulfite conversion of DNAs, the region corresponding to PCR#7 (S7A Fig) was amplified using the primers described in S3 Table. Sequences were aligned using the Kismeth tool [49]. The numbers indicate the plants analyzed, as shown in Fig 7A. Cyto...
Sequences of the different TAD3 copies identified in Nok-1.
SNPs/indels found between chromosomes 1 and 5 are in red. SNPs/indels found between the copies mapped at chromosome 1 are in blue. Stars indicate nucleotides that are identical between all sequences. Bold stars and sequences underlined indicate transcribed regions. Start and stop codons ar...
Methylation patterns of TAD3 in revertant plants.
(A) Schematic representation of the TAD3 gene drawn to scale, PCR#7 and PCR#8 amplicons are positioned. (B) and (C) After bisulfite conversion of DNAs, the two regions indicated in (A) were amplified using the primers described in S3 Table. Sequences were aligned using the Kismeth tool [49]. The num...
PCR#9 is specific for chromosome 5.
(A) Schematic representation of the TAD3 gene drawn to scale, the PCR#9 amplicon is positioned. (B) PCR amplification on genomic DNAs extracted from plants with the indicated genotypes. K1NokK5Col corresponds to plants from the RIL population that are fixed for the Nok-1 allele at chromosome 1 and for the Col-0 a...
Statistics of the sRNA bioinformatics analysis.
(PDF)
Fine mapping of the two loci involved in the incompatibility.
Mapping intervals obtained on chromosome 1 (A) and 5 (B) are indicated. F7 RIL 4RV043 (heterozygous for both incompatible loci localized on chromosome 1 and chromosome 5) was first fixed Nok-1 at chromosome 5 and kept heterozygous at chromosome 1. F7 RIL 4RV355 was already heterozygous a...
TAD3 cDNAs detected in Nok-1.
(A) Expression analysis of TAD3 in Col-0, Nok-1 and Est-1. cDNAs were amplified using primers (described in S3 Table) anchored within the coding region. The numbers of PCR cycles are indicated. ATEF cDNA amplifications served as controls. (B) Region amplified corresponding to the PCRs shown in (A). (C) Sequences of the...
The deletion of 17 bp maps to the incompatible locus on chromosome 1 in Nok-1.
Using primers (IND5.08449F and IND5.08449R) flanking the deletion of 17 bp (Fig 2), 162 plants from the Nok-1 x Col-0 RIL population were genotyped. The shorter fragment (265 bp) is amplified only when RILs are fixed Nok-1 at chromosome 1, confirming that the deletion is...
Sequencing of TAD3-1.
(A) PCR amplification on genomic DNA using the primer set indicated. (B) Genotype differences between Nok-1 and Col-0 obtained by sequencing the PCR fragments shown in (A). Differences (SNPs or INDELs) are indicated. The two changes of amino acid are indicated. Polymorphic regions were sequenced at least three times. The posit...
TAD3 is methylated at chromosome 1 in Nok-1.
(A) PCR fragments specific for chromosome 1 obtained by amplifying genomic DNAs with primers TAD3_K1Nok Forward and Reverse (S3 Table). The forward primer chromosome 1 specific is designed on a short deletion of 7 bp between chromosomes 1 and 5 (S1 Text). (B) DNA methylation of TAD3 at chromosome 1 analy...
Methylation patterns of TAD3-1 in Col-0 x Nok-1 hybrid plants.
After bisulfite conversion of DNAs, the regions corresponding to PCR#9 (S8 Fig) were amplified using the primers described in S3 Table. Sequences were aligned using the Kismeth tool [49]. (A) Results summarized in Fig 5A with Col-0 and Nok-1 parents and the four individual hybrids resul...
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations enabled the investigation of the genetic architecture of gene expression variation. This has the potential to enrich the understanding of the mo...
Aerobic organisms survive low oxygen (O2) through activation of diverse molecular, metabolic, and physiological responses. In most plants, root water permeability (in other words, hydraulic conductivity, Lpr) is downregulated under O2 deficiency. Here, we used a quantitative genetics approach in Arabidopsis to clone Hydraulic Conductivity of Root 1...
cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana access...
Growth is a complex trait that adapts to the prevailing conditions by integrating many internal and external signals. Understanding the molecular origin of this variation remains a challenging issue. In this study, natural variation of shoot growth under mannitol-induced stress was analyzed by standard quantitative trait locus mapping methods in a...
Arabidopsis seeds rapidly release hydrophilic polysaccharides from the seed coat on imbibition. These form a heavy mucilage layer around the seed that makes it sink in water. Fourteen natural Arabidopsis variants from central Asia and Scandinavia were identified with seeds that have modified mucilage release and float. Four of these have a novel mu...
Growth is a complex trait that adapts to the prevailing conditions by integrating many internal and external signals. Understanding the molecular origin of this variation remains a challenging issue. In this study, natural variation of shoot growth under mannitol-induced stress was analyzed by standard quantitative trait locus mapping methods in a...
Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM)...
Sulfur is an essential macronutrient for all living organisms. Plants take up inorganic sulfate from the soil, reduce it and assimilate into bioorganic compounds, but part of this sulfate is stored in the vacuoles. In the first attempt to identify genes involved in control of sulfate content in the leaves we reported that a QTL for sulfate content...
Author Summary
Epigenetics is defined as the study of heritable changes in gene expression that are not linked to changes in the DNA sequence. In plants, these heritable variations are often associated with differences in DNA methylation. So far, very little is known about the extent and stability of epigenetic variation in nature. In this study, w...
QQS expression is negatively correlated with DNA methylation. (A) Schematic representation of the tandem repeats present at the QQS promoter and 5′UTR region. (B) Distribution of DNA methylation at the QQS promoter and 5′UTR sequences. Data is presented as the total number of unmethylated (C) and methylated cytosines (5 mC) in the three sequence co...
Genome-wide analyses of Col-0 and Col-0*. (A) Comparative genomic hybridization (CGH) analysis of Col-0* vs. Col-0 represented as the average of the log 2 ratio of the signal for the INPUT Col-0* over INPUT Col-0. A single normal distribution is observed using the normalmixEM function of the mixtools package on R with an expected number of Gaussian...
Schematic representation of the experimental design used to analyze QQS expression and DNA methylation state in single seed descent lines (named Line A, Line B, Line C and so on) at the S1 and S2 generations.
(TIF)
DNA methylation levels of QQS correlate negatively with QQS expression in natural accessions. (A) Schematic representation of a 30 kb genomic region encompassing QQS. Red arrows indicate McrBC-qPCR primer pairs used to determine DNA methylation levels of TEs flanking QQS; A, B and C represent different primer pairs designed for the same element. (B...
Primer list.
(DOCX)
In higher plants, soluble sugars are mainly present as sucrose, glucose, and fructose [1]. Sugar allocation is based on both source-to-sink transport and intracellular transport between the different organelles [2, 3] and depends on actual plant requirements [4]. Under abiotic stress conditions, such as nitrogen limitation, carbohydrates accumulate...
Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to decompose complex traits like those involved in growth response to the environment. Still, only a few facilities are known to handle individual plants of small stature for non-destructive, real-time phenotype acquisit...
Inferring gene regulatory networks tends to use several biological information. Here we use data from genetic markers and expression data in the framework of discrete static bayesian networks. We compare several scores and also the impact of a network connectivity a priori. We propose and compare two models with existing approaches of gene regulato...
Author Summary
Plants are adapted to soils in which the amounts of different nutrients vary widely, like Zn-deficient or Zn-contaminated soils. Exploring the molecular bases of plant adaptation to Zn-contaminated soils is important in determining strategies for phytoremediation. Here, we describe the mapping and characterization of a QTL for Zn tol...
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...
Chemical complementation links growth defect with soil pH. Increasing soil pH from ∼5 (‘Control’) to ∼6 (‘+CaCO3’) by doubling the amount of CaCO3 mixed to the peatmoss substrate rescues normal vegetative growth of the Shahdara strain.
(TIF)
Multiple accessions sharing the MOT1Sha haplotype confirm the causative gene and polymorphism. Peatmoss phenotype of diverse genotypes is shown: 5 independent Sha-like accessions (Stw-0, Kly-2, Sij-4, Kondara and Zal-3) and F1 plants from complementation crosses between each of these accessions and either the mot1.1 mutant or its wild-type genetic...
Worldwide distribution of functionally contrasted alleles at MOT1. Original collection site and functional MOT1 haplotype (Sha-like in red dots, Ler-like in yellow, Col-like in blue) is shown on a world map for the 102 accessions sequenced in Table S1. Ler-like accessions are found across the whole species known distribution range, while Sha-like a...
Haplotype diversity at MOT1 among 102 accessions. Polymorphisms detected across 102 A. thaliana accessions for the MOT1 locus, including 1 kb upstream (promoter region) and 0.3 kb downstream of the coding region (between blue vertical double-lines). The position (coordinates) of polymorphic bases (regions) are indicated in bp from TAIR10 reference....
Genetic diversity and tests of selection at MOT1 and two reference loci (COI1 and PI).
(XLS)
Detailed results of HKA simulations.
(XLS)
Fine-mapping the causative locus identifies MOT1 as a candidate gene. A. The physical region of chromosome 2 found to be linked to the growth defect phenotype is shown (physical positions are given in Mb). B. Zooming in the candidate region highlights recombinants within the inbred lines that allow to fine-map the causative locus, thanks to additio...
MOT1Sha is able to transport Mo in yeast. The Sha allele of MOT1 was overexpressed in yeast heterologous system (Sha/p416) and shown to lead to Mo accumulation compared to the empty vector (p416, used as reference) or the yeast wild-type strain (BY4741), to an extent not significantly different from the Col MOT1 allele (Col/p416). Error bars repres...