Biology subjects

Cornille, A. M.

Publications and source records attributed to Cornille, A. M..

3 recordsLinked to original sources

bioRxiv2026

Domestication altered defense responses and host-aphid interaction networks in apples

- Domestication can profoundly reshape plant defense strategies and host-parasite interactions, but its consequences for resistance and coevolution in perennial crops remain poorly understood. We investigated how domestication altered apple responses to its major pest, the rosy apple aphid (Dysaphis plantaginea). - We compared wild (Malus orientalis, two geographically differentiated M. sylvestris populations) and cultivated (cider and dessert M. domestica) apple genotypes against two genetically distinct aphid genotypes, combining controlled infestation experiments with phenotypic measurements, paired host-aphid RNA-seq, co-expression network analysis, and genome-wide selection scans. - Aphid fitness and host resistance varied strongly across host populations: domesticated apples supported higher aphid performance, whereas Romanian M. sylvestris showed the highest resistance, revealing marked host-aphid genotype-specific asymmetric compatibility. Cultivated apples have developed extensive inducible transcriptional defense responses, whereas wild populations showed weaker perturbation despite lower aphid fitness, consistent with more constitutive defense. Host-aphid co-expression analyses identified candidate coevolutionary modules linking host resistance genes under balancing selection with aphid genes under positive selection. - Together, these results demonstrate that apple domestication reshaped defense-associated regulatory networks and modified the adaptive landscape experienced by aphid populations, providing new insight into the evolutionary consequences of perennial crop domestication on host-parasite interactions.

evolutionary biology↗

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↗

bioRxiv2025

Genomic architecture of the self-incompatibility locus in apple provides insights into the evolution of collaborative non-self recognition

Self-incompatibility (SI) systems prevent self-fertilization, thereby maintaining genetic diversity in flowering plants. Among them, collaborative non-self recognition (CNSR) is the most widespread, yet the genomic organization and evolutionary maintenance of its multigenic recognition system remain poorly understood. Using 27 haplotype-resolved genomes from wild and domesticated apples (Malus spp.), we dissected the structure and evolution of the S-locus. We identified 17 S-RNase alleles and 500 pollen-expressed S-locus F-box brother (SFBB) genes across 18 families. The S-locus shows extensive structural divergence among alleles and transposable element accumulation, consistent with long-term restricted effective recombination. Despite this divergence, haplotypes carrying the same S-RNase allele retain remarkably conserved SFBB repertoires and gene organization, even across species boundaries, indicating that long-term balancing selection preserves highly conserved S-haplotype architectures associated with specific S-RNase lineages. Tandem duplication, positive selection, and signatures consistent with gene conversion contribute to the diversification of pollen-expressed SFBB genes while S-RNase-associated SFBB repertoires remain conserved across haplotypes carrying the same S-RNase allele. Our results reveal how a structurally dynamic yet evolutionarily constrained genomic region can sustain long-term S-allele diversity and preserve complex multigenic haplotype architectures in flowering plants.

genomics↗