Abstract This is the first report evaluating the genetic diversity of Mexican grape species utilizing DNA-based markers to understand the distribution of grape species, and patterns of hybridization. The study utilized accessions maintained in three collections in Mexico, one in the USA and recently collected germplasm. Fifteen SSR markers were used to develop a fingerprint database to identify unique germplasm. Two different clustering analyses without prior population assignment, were used to identify groups that were verified by a Discriminant Analysis of Principal Components and a Principal Coordinate Analysis. Genetic diversity estimates were made across and within groups to validate the results obtained from the clustering analyses. Multiple clustering analyses and diversity parameters supported six genetic groups representing different geographic regions. The Northeastern group was the most diverse with a geographic range extending to Eastern and Central Mexico, while the Coahuila group was the least diverse. Vitis arizonica Engelm. and Vitis cinerea Engelm. ex Millardet were the most abundant species with many hybrid forms. We provide evidence that wild grape species in Mexico follow the physical barriers of mountain ranges like the Sierra Madre Oriental with an east–west divide and the Trans-Mexican Volcanic Belt as a corridor for gene flow among different grape species. Additional collections are required to fully understand the extent of hybridization and to clarify hybrid zones.

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Conclusion

This is the first assessment of genetic diversity of Mexican wild grape species based on SSR marker fingerprint data and provides a framework to manage unique germplasm in different collection sites in Mexico. Population structure and genetic diversity analyses identified six genetic groups that are separated by mountain ranges of the Sierra Madre Oriental with an east–west divide and the Trans-Mexican Volcanic Belt act as a corridor for gene flow among different grape species. Vitis cinerea was the most prevalent species with a large geographical range. It hybridizes with other native species like V. bloodworthiana to the western side, and with V. tiliifolia to the east, possibly forming other types that are difficult to identify solely by their morphological features. Clustering analyses and diversity indices indicated that the Coahuila and Chihuahua genetic groups were more isolated and morphological features revealed them to be pure forms of V. arizonica and its hybrids. Additional grape germplasm from different parts of Mexico is needed to identify the extent and spread of different grape species, and to identify hybrid zones and their role in grape speciation. This study attempts to highlight the importance of Vitis conservation not only for grapevine breeding, but ecosystem services wild grapevines serve to the Mexican indigenous communities.