Clonal domestication and biocultural erosion in tequila agave ( Agave tequilana Weber var. azul )

Background and Aims Tequila agave (Agave tequilana Weber var. azul) sustains one of the world’s most valuable spirits industries, yet its domestication history and genetic status remain incompletely understood. Historical and ethnobotanical evidence indicates that tequila was once produced from multiple A. tequilana landraces that have been largely replaced by a single clonal cultivar. We used genome-wide data to reconstruct the domestication history of tequila agave, quantify genetic diversity across cultivated, landrace, and wild relatives; and determine whether independent clonal propagation generated genetic differentiation within the modern cultivar. Methods We combined extensive field surveys across the Tequila Denomination of Origin with genotyping-by-sequencing (GBS) of 92 accessions, including tequila agave, remnant A. tequilana Weber landraces, and wild and managed taxa from the Agave angustifolia complex. Genome-wide SNPs were used to assess population structure, genetic diversity, domestication relationships, and differentiation among lines maintained by different tequila producers. Key Results Genome-wide analyses confirmed that A. tequilana is a domesticated derivative within the A. angustifolia complex. Modern tequila agave forms a highly homogeneous but not invariant lineage, retaining genetic variation likely preserved through long-term clonal propagation. Traditional landraces exhibited substantially greater genetic diversity and occupied intermediate positions along a domestication continuum from wild A. angustifolia to tequila agave. Despite extensive fieldwork, landraces were found to persist only as isolated ornamental individuals. We detected subtle genetic differentiation among tequila agave lineages maintained by different producers. Conclusions Tequila agave represents an extreme example of clonal domestication where industrial production and regulatory frameworks have driven profound genetic and biocultural erosion. Although clonal propagation buffered the complete loss of genetic variation, the near disappearance of traditional landraces eliminated unique domestication-associated diversity. Rescuing remnant landraces and wild relatives is essential to preserve evolutionary potential, enhance crop resilience, and support the long-term sustainability of tequila production.