Biology subjects

Dapena, E.

Publications and source records attributed to Dapena, E..

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↗

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↗

bioRxiv2025

Gene flow from the European wild apple and selection shaped the domesticated apple (Malus domestica Borkh.) genome

How selection and demography shape genomes of long-lived crops remains largely unresolved. Using apple (Malus domestica) as a model, we integrate 218 whole genomes (68 cultivated dessert/cider; 150 wild: M. sieversii, M. orientalis, M. sylvestris), RNA-seq, and a flowering-time GWAS to resolve how these forces forged the cultivated apple genome. Despite weak neutral differentiation and widespread admixture, dessert and cider apples form distinct gene pools that derive primarily from M. sieversii-M. orientalis rather than European M. sylvestris. We find no evidence of a strong domestication bottleneck, as expected in perennials. Demography-aware selection scans reveal largely non-overlapping targets: dessert shows more hard sweeps at genes linked to fruit quality, disease resistance, and flowering, whereas cider shows proportionally more soft sweeps and balancing selection; RNA-seq differential expression supports these candidates. Wild-to-crop introgression from M. sylvestris is extensive but heterogeneous by context: some introgressed tracts concentrate in hard-sweep regions and approach fixation (consistent with rapid, targeted uptake), whereas others persist at intermediate frequencies with soft-sweep signatures (consistent with diffuse, recurrent introgression of adaptive alleles). Extending to the phenotype, the lead chromosome 9 flowering-time association lies within an introgressed segment near a transposable element and is separated from sweep peaks, consistent with regulatory/polygenic control. Cultivated apples carry a lower predicted deleterious load than wild relatives. Together, these results provide one of the most comprehensive population genomic portraits of a perennial fruit tree domestication, clarifying how selection and adaptive introgression jointly shaped the cultivated apple genome architecture and yielding actionable targets for breeding and conservation. Significance statementPerennial crops are underexplored compared to annuals, leaving open the question of how selection, gene flow, and demography shape their genomes. Using the apple tree (Malus domestica), we analyzed 218 genomes, along with expression and trait data. Despite weak genome-wide differences, dessert and cider apples form distinct gene pools. Widespread gene flow from the European wild apple supplied adaptive alleles, with contrasting dynamics: in cider, a few introgressed DNA segments rose rapidly; in dessert, many variants shifted gradually. Cultivated apples also carry a lower predicted burden of harmful mutations than wild relatives. Together, these results redefine perennial domestication and pinpoint genomic targets to accelerate breeding and conservation.

genetics↗