Biology subjects

Loudet, O.

Publications and source records attributed to Loudet, O..

8 recordsLinked to original sources

bioRxiv2025

Dissecting the genetic basis of drought escape across multiple traits in colonizing Arabidopsis thaliana lineages

Drought response in plants is complex, involving integration across a range of physiological processes. However, our knowledge of how different aspects of drought response are linked at the genetic level is limited. We investigated multi-trait adaptation in Arabidopsis thaliana from the Cape Verde Islands (CVI). Using a high-throughput phenotyping platform that minimizes spatial heterogeneity, we measured variation in rosette area, growth rate, leaf color, water-use efficiency (WUE), and stomatal patterning under precisely controlled water conditions. Relative to the Moroccan outgroup, CVI populations evolved to be smaller rosette size with faster growth and reduced WUE, consistent with drought escape adaptation. Genome-wide association mapping revealed evidence for pleiotropy involving MPK12 (WUE, rosette area, growth rate, and leaf color), NHL26 (WUE and leaf color), SUVH4 (stomatal patterning, rosette area, and leaf color), and FRI (WUE and leaf color), along with an enrichment of signals in ABA response. This study advances our knowledge of the genetic mechanisms driving plant adaptation to novel precipitation environments. By identifying key genetic components and their contributions to multi-trait adaptation, our findings offer insights into how plants respond to environmental challenges and contribute to predicting plant responses to future climate change.

genomics↗

bioRxiv2024

Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature

Loss of DNA methylation over transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritance are unknown. Here, we demonstrate at thousands of TE loci across the Arabidopsis thaliana genome, that experimentally-induced hypomethylation can be transmitted transgenerationally and reveal the role of small RNAs derived from related copies in counteracting this transmission. Using data from >700 strains collected worldwide, we uncover natural hypomethylation at hundreds of the same TE loci, often situated near stress-responsive genes. Like their experimental counterparts, most natural epivariants we tested can be inherited without DNA sequence changes and are therefore bona fide epialleles, although genetic factors modulate their recurrence or persistence. Crucially, we demonstrate that TE-mediated epiallelic variation associated with differential gene expression is generally causal and may be target of selection in specific environments, thus establishing its importance in nature.

genomics↗

bioRxiv2024

Parallel Evolution of Salinity Tolerance in Arabidopsis thaliana Accessions from Cape Verde Islands

Soil salinization poses a significant threat to crop production impacting one fifth of all cultivated land. The Cape Verde Islands are located 600 km from the coast of Africa and are characterized by high salinity soils and inland water sources. In this study we find that Arabidopsis thaliana plants native to these islands accumulate a metabolite that protects them from salt stress. We partially characterized this metabolite as glucuronyl-mannose. We find that the ability to produce glucuronyl-mannose evolved independently in two different islands from the same archipelago through mutations in the same gene, an alpha glycosidase protein that we named GH38cv. These cases of parallel evolution suggest positive selection towards the increase of salt tolerance with low fitness costs. Indeed, plants carrying derived alleles of GH38cv do not present growth defects or low defenses under normal conditions, but show better germination rates, longer roots and better hydric status than non-mutated plants when exposed to salt stress. These findings provide a knowledge-based method to develop salt resilient crops using natural mechanisms, which could be attractive both to conventional and organic agriculture.

plant biology↗

bioRxiv2020

The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana

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 crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions which included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently co-exist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

evolutionary biology↗

bioRxiv2019

Transcriptional natural variation at FLM induces synergistic pleiotropy in Arabidopsis thaliana

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 classical quantitative genetics on a recombinant inbred line population derived from a Can-0 x Col-0 cross, we identified the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation for leaf growth and colour. Interestingly, we showed that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation observable across thousands of plant species. We demonstrated that the functional differences at FLM relies on a single intronic substitution, disturbing transcript splicing and leading to a low expression of the active FLM transcript. Using phenotypic and climatic data across Arabidopsis natural populations, our work shows how noncoding genetic variation of a single gene may be adaptive through synergistic pleiotropy.

plant biology↗

bioRxiv2018

Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis

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 stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana. Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.

plant biology↗

bioRxiv2018

The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana

One of the main outcome of quantitative genetics 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 age... Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to push back the limits of our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping resolution was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.

genetics↗

bioRxiv2017

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

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, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

genomics↗