Genotype–Environment Association and Climate Change Vulnerability of the Economically Important Crop Wild Relative Agave Angustifolia Haw

BACKGROUND AND AIMS: Crop wild relatives (CWR) are an important source for crop improvement, but they are often threatened by overharvesting and habitat fragmentation. This is the case for Agave angustifolia, one of the most important CWRs of cultivated agave species in the tequila and mezcal industries. Despite its cultural and economic importance, no range-wide genomic assessments exist for this species. METHODS: We analyzed double-digest genotyping-by-sequencing (GBS) data from 215 wild individuals from 67 populations spanning the entire Mexican distribution range of A. angustifolia. We combined newly generated data (97 individuals) with previously published sequences (118 individuals). We combined genomic data with species distribution models for past and future climatic scenarios, performed environmental association and genomic offset analyses, and tested spatial versus environmental drivers of differentiation. KEY RESULTS: In terms of climate and genomic offset, we found that although some populations-especially coastal ones-are expected to experience a considerable challenge adapting to changing environments, the species as a whole is likely to benefit from the warmer, drier conditions predicted by climate change projections. We identified specific wild populations that harbour climate-adapted alleles and are best positioned for persistence and crop improvement. While contemporary populations showed moderate-to-high genomic diversity, recent demographic impacts from wild harvest and local cultivation may not yet be detectable due to the species' long generation time and vegetative propagation. Genome-wide divergence among A. angustifolia populations was driven by Pleistocene climate oscillations and isolation-by-environment. CONCLUSIONS: Our study highlights both resilience and risk across the range of A. angustifolia, providing a comprehensive genetic framework for conserving its adaptive potential in the face of environmental change.