Biology subjects

Bazot, S.

Publications and source records attributed to Bazot, S..

3 recordsLinked to original sources

bioRxiv2026

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

Climate-associated genomic variation is often used as a proxy for adaptive potential, yet whether it reflects adaptation with phenotypic consequences, rather than demography alone, is rarely tested in long-lived species. Genomic offsets forecast climate maladaptation from genotype-environment models but are seldom validated against phenotypes. We combined whole-genome resequencing, SNP and transposable element insertion polymorphism (TIP) variation, landscape genomics, genome-wide association, genomic offset, and common-garden phenotyping in the European wild apple (Malus sylvestris Mill.), a crop wild relative with a complex demographic history, to test this. Results: Of 148 resequenced accessions (135 wild, 13 cultivated), 89 wild individuals formed the core dataset. Population structure was associated with Last Glacial Maximum precipitation rather than contemporary climate, and genetic diversity increased from west to east. Genome-environment associations across 9.75 million SNPs identified climate-associated loci enriched in photoperiod-related flowering-time genes, with limited overlap with phenotype-associated loci. SNP-based genomic offset was associated with bud-break timing in the Saclay common garden (marginal R2 = 0.31), with higher offsets corresponding to earlier bud break, but not with growth or ecophysiological traits. This association depended on Austrian and Romanian populations and was clearest in non-admixed wild individuals. Offsets based on TIPs or glacial climate did not predict measured phenotypes. Conclusions: Climate association, phenotypic relevance, and predictive power of genomic variation are separable. In a long-lived tree, genomic offset predicted spring phenology, a key adaptive trait, but this signal varied across provenances and ancestries and was absent for transposable elements. Genomic offsets can therefore forecast potential phenological maladaptation, provided they are validated against phenotypes such as bud break.

ecology↗

bioRxiv2026

Climate drives plasticity and genetic adaptation in apple trees

BackgroundPerennial crops respond to climate change through phenotypic plasticity and local adaptation, yet how these responses are orchestrated at the molecular level and reshaped by domestication remains poorly understood. ResultsWe grew 1,249 seedlings from five populations of M. domestica, M. orientalis, and M. sylvestris under four simulated European climates, quantified 12 phenotypic traits, performed RNA sequencing on 96 individuals, and integrated these data with previously published genome-wide polymorphism data from M. sylvestris to disentangle conserved climate responses from local adaptation. Climate was the dominant driver of phenotypic and transcriptional variation, revealing 344 conserved climate-responsive genes enriched for stress responses, nutrient metabolism, and cell wall biosynthesis. These genes are under strong purifying selection and carry fewer deleterious mutations. In contrast, genome-environment association analyses identified 217 loci associated with temperature and precipitation gradients, only a subset of which showed climate-responsive expression and elevated genomic differentiation. Population-level expression divergence closely mirrored neutral genetic differentiation, indicating that most transcriptomic divergence reflects demographic history rather than adaptive regulatory evolution. Domestication reshaped molecular diversity and mutation load without disrupting the conserved climate-response program. ConclusionsClimate responses in apple are primarily mediated by an evolutionarily conserved transcriptional program maintained by strong purifying selection, whereas local adaptation relies on largely distinct, population-specific loci. These findings reveal that conserved plasticity constitutes the dominant molecular response to climatic variation, whereas local adaptation contributes a secondary, population-specific layer of evolutionary change.

evolutionary biology↗

bioRxiv2022

Contribution of deep soil layers to the transpiration of a temperate deciduous forest: quantification and implications for the modelling of productivity

Climate change is imposing drier atmospheric and edaphic conditions on temperate forests. Here, we investigated how deep soil (down to 300 cm) water extraction contributed to the provision of water in the Fontainebleau-Barbeau temperate oak forest over two years, including the 2018 record drought. Deep water provision was key to sustain canopy transpiration during drought, with layers below 150 cm contributing up to 60% of the transpired water in August 2018, despite their very low density of fine roots. We further showed that soil databases used to parameterize ecosystem models largely underestimated the amount of water extractable from the soil by trees, due to a considerable underestimation of the tree rooting depth. The consensus database established for France gave an estimate of 207 mm for the soil water holding capacity (SWHC) at Fontainebleau-Barbeau, when our estimate based on the analysis of soil water content measurements was 1.9 times as high, reaching 390{+/-}17 mm. Running the CASTANEA forest model with the database-derived SWHC yielded a 350 gC m-2 y-1 average underestimation of annual gross primary productivity under current climate, reaching up to 700 gC m-2 y-1 under climate change scenario RCP8.5. It is likely that the strong underestimation of SWHC that we show at our site is not a special case, and concerns a large number of forest sites. Thus, we argue for a generalisation of deep soil water content measurements in forests, in order to improve the estimation of SWHC and the simulation of the forest carbon cycle in the current context of climate change. HighlightsO_LIForest-atmosphere carbon exchanges remained insensitive to record drought. C_LIO_LIDeep soil (150-300 cm) provisioned up to 60% of the water transpired by the forest during drought. C_LIO_LISoil databases were underestimating soil water holding capacity by a factor of two. C_LIO_LISimulated forest productivity is strongly sensitive to soil water holding capacity parameter. C_LIO_LIDeep soil water content measurements are urgently needed to correctly estimate the soil water holding capacity. C_LI

ecology↗