Genome-wide assessment of genetic variation and population structure in cultivated vanilla from Madagascar

Madagascar dominates the international vanilla market with Mexican Vanilla planifolia introduced from Reunion Island 150 years ago. A breeding program was established 80 years ago, incorporating local and imported wild and cultivated progenitors of several vanilla species. Presumably, some resulting genotypes were released and may be still found within plantations, where some morphological variability may be encountered. To provide an overview on the extent of the genetic diversity of the unexplored cultivated vanilla in Madagascar, 272 accessions from the four major cultivation areas were collected. Six morphological groups were identified: Vanille Banane, Big Vanilla, Tsivaky, Vanilla planifolia, V. pompona and a group intermediate to both previous ones. ddRAD-seq protocol was used to generated 17,948 high-quality SNPs, proportionally distributed across the 14 chromosomes of V. planifolia with a coverage of 43.8X. High genetic diversity was found (Ho = 0.44). Principal component analysis (PCA) and NeighborNet analysis separated the morphological groups from each other. Vanille Banane and Big Vanilla were the most distant groups. The morphologically intermediate group exhibited genetic differentiation into two sub-groups, including original cultivars, locally referred to as “Tsitaitra”, arising from the past breeding program. Results highlighted differentiation in taxonomy, phenotype, region of provenance and ecology. The genetic structure of V. pompona accessions was consistent with their provenance and altitude in the SAVA region. Big Vanilla was found exclusively at the low altitude areas of Mananara Nord, whereas the two intermediate genetic sub-groups occurred predominantly at the low and high altitudes of Manakara. We emphasize the influence of the ancient breeding program and human intervention on Madagascar’s genetic resources distribution. This study provides valuable data that should support future vanilla breeding and management programs in Madagascar.