Landscape Genomics of Wild Olive Informs Cultivar (Mal)adaptation via Cultivar Genomic Offset

Perennial crops’ wild relatives provide locally adapted germplasm for identifying genomic signatures of environmental adaptation. Such insights, assuming shared adaptive variation between wild and cultivated compartments, can improve predictions of cultivar adaptive potential and guide cost-effective multi-location field trials for long-lived species such as olives. We analyzed 27 wild olive (Olea europaea subsp. europaea var. sylvestris) populations across a 13° latitudinal gradient in the western Mediterranean (southern France, Corsica, Spain, Morocco). Genetic structure analyses identified genuinely wild genotypes likely to harbor locally adapted variation, later used for genotype-environment association (GEA) studies. Environmental Niche Modelling (ENM) and redundancy analysis (RDA) were combined to construct a landscape genomic model anchored in the species’ current ecological niche. This model was then used to estimate the spatial Genomic Offset of cultivated olives, a framework we term Cultivar Genomic Offset. Predictions revealed a latitude-dependent correspondence between cultivar environments and adaptive genomic regions. In a Moroccan common garden, early-flowering cultivars requiring less winter chilling showed lower local Cultivar Genomic Offset values than late-flowering ones, indicating stronger adaptation to local conditions. These results underscore the value of wild germplasm for uncovering adaptive genomic variation that can ultimately inform the resilience of cultivated populations