Biology subjects

Brachi, B.

Publications and source records attributed to Brachi, B..

7 recordsLinked to original sources

bioRxiv2025

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

Local adaptation has been demonstrated in many organisms, but the traits involved, and the temporal and spatial scales at which selection acts are generally unknown. We carried out a multi-year study of 200 accessions (natural inbred lines) of Swedish Arabidopsis thaliana using local field sites and a combination of common-garden experiments that measured adult survival and fecundity, and selection experiments that measured fitness over the full life cycle. We found evidence of strong and variable selection, with particular genotypes favored more than five-fold in certain years and locations. Fecundity showed evidence of classical local adaptation, with accessions generally performing better closer to their home. However, relative to other accessions, southern ones usually had the highest fecundity---but were far more sensitive to harsh winters and slug herbivory, which strongly decreased both survival and fecundity. Furthermore, accessions originally sampled on beaches had low fecundity in all common-garden experiments, but massively outperformed all other accessions in the selection experiments, presumably due to an advantage during seedling establishment associated with their very large seeds. We conclude that local adaptation in A. thaliana reflects strong temporally and spatially varying selection on multiple traits, generally involving trade-offs and different life-history strategies, making fitness difficult to predict and measure.

genetics↗

bioRxiv2023

Species-specific epigenetic responses to drought stress of two sympatric oak species reflect their ecological preferences.

O_LIIn a context of climate change, it is necessary to decipher the strategies established by plants to cope with limited water supply. C_LIO_LITranscriptome, methylome and small RNA data were generated for two oak species with contrasting levels of drought tolerance (Quercus robur and Quercus petraea), under control and drought stress conditions C_LIO_LIAll data are in line with a species-specific response to drought stress consistent with their ecological preferences. The biological processes associated with genomic regions identified in all datasets were mainly associated with parietal processes in Q. petraea, which may explain in part its better tolerance to water deprivation. C_LIO_LIA significant proportion of DNA methylation differences observed in control conditions between the two oak species were maintained during DS which may constitute a pool of epigenetic markers discriminating these two oak species. These markers were enriched in highly differentiated SNPs suggesting that some of them may be associated both with the ecological differences or intrinsic barriers to reproduction between the two species. C_LIO_LIAn integrative approach of the three datasets revealed genomic co-locations of potential importance for forest three adaptation to drought stress. C_LI

genomics↗

bioRxiv2023

Extensive variation of leaf specialized metabolite production in sessile oak (Quercus petraea) populations is to a large extent genetically determined but not locally adaptive.

Specialized or secondary metabolites play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaks Quercus petraea, phenolics contribute to reduce herbivore damage and improve drought resistance. Here, we explored the natural variation of specialized metabolites in nine European provenances of sessile oaks and aimed to detect its underlying genetic bases. We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 217 specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype individuals for 1.4M genetic markers. We found that leaf specialized metabolites displayed extensive within-provenance variation, but very little differentiation between provenances. In addition, a genome-wide association study allowed detecting significant associations for 42% of these metabolites. Hence, our results suggest that genetic variation for most leaf specialized metabolites is unlikely to be locally adaptive, however lack of differentiation among populations suggests selection acts locally to maintain diversity at loci associated with leaf specialized metabolites variation.

evolutionary biology↗

bioRxiv2021

Water stress-associated isolation barriers between two sympatric oak species

Drought and waterlogging impede tree growth and may even lead to tree death. With climate change, these environmental factors are a growing source of concern, particularly for temperate forests. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species -- pedunculate oak (PO) and sessile oaks (SO) -- have overlapping ranges, but are highly constrained locally by soil water content variation. These differences in local ecological requirements provide a powerful biological model for studying the role of ecological barriers in speciation. We used an experimental set-up mimicking the ecological preferences of these species, in which seedlings were subjected to waterlogging and drought. We studied gene expression in roots by RNA-seq and identified genes differentially expressed between treatments with different outcomes depending on species. These "species x environment"-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with expression profiles presenting a "species" effect regardless of imposed constraints with important roles in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the candidate genes were enriched in highly differentiated SNPs. This suggests that many of the genes involved in the contrasting transcriptomic responses are subject to natural selection and that gene regulation helps to maintain these two different oak species in sympatry.

plant biology↗

bioRxiv2021

Extreme climatic events but not environmental heterogeneity shape within-population genetic variation in maritime pine

How evolutionary forces interact to maintain quantitative genetic variation within populations has been a matter of extensive theoretical debates. While mutation and migration increase genetic variation, natural selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e. experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from spatially heterogeneous environments. We used phenotypic measurements of five growth, phenological and functional traits from three clonal common gardens, consisting of 523 clones from 33 populations of maritime pine (Pinus pinaster Aiton). Populations from harsher climates (mainly colder areas) showed lower genetic variation for height in the three common gardens. Surprisingly, we did not find any association between within-population genetic variation and environmental heterogeneity or population admixture for any trait. Our results suggest a predominant role of natural selection in driving within-population genetic variation, and therefore indirectly their adaptive potential.

evolutionary biology↗

bioRxiv2017

Plant genes influence microbial hubs that shape beneficial leaf communities

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTUs. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.

microbiology↗

bioRxiv2017

Genetic variants affecting plant size and chemical defenses jointly shape herbivory in Arabidopsis

Herbivorous insects exhibit strong feeding preferences when choosing among plant genotypes, yet experiments to map loci mediating plant susceptibility to herbivory rarely incorporate host choice. To address this gap, we applied genome-wide association (GWA) mapping to uncover genetic polymorphisms mediating damage from foraging insects (two populations of Scaptomyza flava) across a mixture of Arabidopsis thaliana genotypes in experimental enclosures. The effect of chemical defenses (glucosinolates) on herbivory depended on herbivore genotype. Unlike many studies that minimize the effects of host choice behavior, we also found a large effect of plant size on herbivory--likely through its effect on plant apparency--that was independent of herbivore genotype. These herbivory-associated loci are polymorphic at fine spatial scales, and thus have potential to shape variation in herbivory within natural populations. We also show that the polymorphism with the largest effect on herbivory underlies adaptive latitudinal variation in Arabidopsis plant size across Europe. Overall, our results provide genetic support for ecological observations that variation in both chemical defenses and non-canonical defense traits (e.g., plant size and phenology) jointly shapes plant-herbivore interactions.

plant biology↗