Klimova, A.; Gutierrez Rivera, J. N.; Aguirre-Planter, E.; Eguiarte, L. E.

Plant domestication in Mesoamerica gave the world crops of global significance, such as maize, beans, squashes, cocoa, and cotton. Additionally, it has introduced species of regional economic importance, which still display intermediate levels of domestication, including Agave, Opuntia, columnar cacti, Amaranthus, and various ornamental species. Agaves, in particular, hold immense cultural and economic significance in Mexico and play a crucial ecological role in wild plant communities. However, current agricultural practices have negatively impacted both wild populations of agave through overexploitation and habitat destruction, as well as cultivated plants by reducing available landraces and promoting the use of homogeneous plant material. Using genomic data (RADseq) and over 50,000 SNPs, we aimed to assess how local social and political decisions may have influenced genomic diversity and differentiation in intensively managed, clonally propagated Agave angustifolia (Espadin) in the state of Oaxaca, as well as in the cultivated A. angustifolia used to produce mezcal known as Bacanora in the state of Sonora and their wild counterparts from both regions. We found evidence suggesting that Espadin recently aroused through farmer selection of a clonal lineage with desirable mezcal production attributes (i.e., hybrid vigor), apparently from a cross between genetically distinct wild populations or by hybridization between wild and cultivated varieties. Espadin samples were represented by closely related heterozygous genotypes, with considerable genetic differentiation from wild plants. On the other hand, the genomic composition of cultivated Bacanora agave apparently was influenced by a recently lifted ban (in 1992) on its cultivation and distillation, which, along with the relatively lower popularity of this beverage, allowed cultivated Bacanora agave to maintain the genetic diversity found in wild populations of the regions. We found that social and political decisions may have important impacts on crop genomic diversity and differentiation.