Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia

Abstract

PremiseThe central Oaxaca Basin has a century‐long history of agave cultivation, and it is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as “espadín” is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades‐long clonal propagation has affected its genetics.MethodsUsing RADseq and over 8,000 SNPs, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations.ResultsGenetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation.ConclusionsThe considerable heterozygosity found in “espadín” is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.This article is protected by copyright. All rights reserved.

Differences in the genomic diversity, structure, and inbreeding patterns in wild and managed populations of Agave potatorum Zucc. used in the production of Tobalá mezcal in Southern Mexico

“…In this species, similar management practices to Tobala ´are used (i.e., incipient management and the introduction of plants and seeds from the wild). Our heterozygosity results were also similar to those reported using RADseq for the wild A. angustifolia from Oaxaca (H E = 0.24), but lower than those founded in the cultivated A. angustifolia known as "Espadı ´n" (H E = 0.29) [68]. This last difference may result from different type of management practices between A. angustifolia "Espadı ´n" and A. potatorum.…”

“…In addition, A. potatorum has cross-pollination and usually reproduces only by seed and not clonally. Thus, we did not observe an excess of heterozygosity related to long-term clonal propagation found in other Agave species such as A. tequilana [7] and A. angustifolia [68].…”

“…We found a negative inbreeding index, indicating an excess of heterozygotes in two cultivated populations (SV2-C y Mat-C), and five wild localities (Cu7-W, Cu3-W, Ix-W, SJR5-W, SV1-W). In previously published works on the Agave genus, negative F IS values have been found, especially in cultivated individuals of intensively managed species, such as A. tequilana F IS = -0.042 [7] and A. angustifolia "Espadı ´n" F IS = -0.07 [68]. These values have been related to artificial selection for hybrid vigor and an accumulation of somatic mutations in the genome.…”