Within the Vanilla genus, leaflessness has evolved as an adaptation to heat and drought conditions. Bioclimatic factors have been shown to be responsible for the ecologically driven speciation of seven leafless Vanilla species indigenous to Madagascar. In the present study, we further assessed whether some of these species could be good models for genome-environment associations (GEA) studies at the intraspecific level, in order to later identify genomic signatures of adaptation, which may be useful in vanilla crop breeding for abiotic stress tolerance. For this, we selected two target species in Madagascar, V. perrieri and V. bosseri, as they are the most widely distributed, spanning over different bioclimatic regions. Principal component analysis (PCA) of 19 environmental variables revealed a bioclimatic structure based on sample collection sites. We also assessed intraspecific genetic variation using previously generated data from seven microsatellite loci. For each species, redundancy analyses demonstrated that environmental variations (temperature, precipitation, and vegetation index) contributed to the genetic structure of the populations through isolation-by-environment (IBE). These results indicate local adaptation of the populations of these two species and suggest that they represent appropriate models for further studying the climatic adaptation of vanilla plants.

Wild vanilla populations with high aromatic potential and morphological affinity to Vanilla odorata have been identified in Oaxaca, Mexico. This study employed morphologic and molecular taxonomic approaches to characterize plant material collected from the field and subsequently maintained under uniform conditions at the Tecnológico Nacional de México Tuxtepec campus germplasm bank. Morphological characterization of the three populations was conducted, and genetic analyses of 155 accessions (2365 SNPs) were performed using Genotyping by Sequencing. The morphological analyses revealed clear differences in vegetative and reproductive traits among the studied accessions. Phylogenetic and STRUCTURE analyses identified three groups within the V. odorata-like clade: a pure group, and two hybrid groups involving V. odorata and V. insignis or V. cribbiana. These findings reveal a high level of phenotypic and genetic diversity within wild vanilla populations from Oaxaca and suggest that hybridization may have played an important role in the evolutionary history of the group. Furthermore, the results challenge the current taxonomic circumscription of Vanilla odorata, indicating that its taxonomic identity and evolutionary origin require re-evaluation. This study provides new insights into the diversification and taxonomy of aromatic wild vanilla species in Mesoamerica.