Genetic diversity of the cultivated vanilla in Madagascar by Léa Onisoa Rivo Rasoamanalina

Natural vanillin extracted from cultivated vanilla pods is the most common flavour in the world, and the vanilla crop is crucial to Madagascar's socio-economy, providing a direct livelihood for over 80,000 families and representing the majority of the country's exports. However, local production has been threatened by fungal diseases since before 1932. A breeding program (from 1944 to 2000) showed the potential for developing resistant vanilla varieties, which gave hope for a sustainable vanilla production. Unfortunately, the program has been abandoned, and since then, no genetic studies of the cultivated vanilla in Madagascar have been conducted. The classical genetic marker systems such as isozymes, RAPD, RFLP, microsatellites, previously used in cultivated vanilla did not successfully allow to determine the diversity and structure of this germplasm. The aim of the present work was to evaluate the current genetic resources of the cultivated vanilla in Madagascar. A large-scale prospect was conducted to cover as much diversity present in Madagascar as possible, including the four major vanilla production regions distributed from north to south and northwest of the country. The sampling also covered various environmental conditions for vanilla cultivation in Madagascar. SNP discovery and genotyping were achieved using the double digest restriction-site associated DNA (ddRADseq) protocol. The 17,948 developed high-quality SNPs revealed a clear genetic structure of the Malagasy germplasm and highlighted the presence of original varieties, mainly arising from the past breeding program. The 246 accessions from the field were clustered into five genetic groups – Vanilla planifolia, V. pompona, Big Vanilla and two intermediary groups phenotypically close to each other and intermediate between the two first groups. Two additional genetic groups were identified in a local germplasm collection. Intra-species genetic structuration was also revealed within the main cultivated species – V. planifolia – structured into 3 major genetic groups with higher variability than expected. However, the genetic distances between the groups was low. Redundancy analysis detected a low contribution of spatial and environmental parameters to the variation of SNPs. Therefore, many other unincluded parameters may contribute to the diversity of SNPs. This is the first genetic investigation of the cultivated vanilla in Madagascar providing relevant data on genetic structure and diversity that offer valuable information for future breeding and management programs.