Société Française de Bioinformatique

Mots-Clés

Bio-analyses Population genomics Biogeography Crop diversity Molecular Evolution

Description

The greater yam (Dioscorea alata L.) is the most widespread edible yam species and is cultivated throughout sub-tropical and tropical areas (Hahn 1995). The species strongly contributes to food security in West Africa, where its production is expanding because of its ease of cultivation, in the Caribbean and the Pacific where it has considerable social and cultural importance, and also in parts of upland Asia (Lebot 2009). Despite of its importance and the release of different genome references (Bredeson et al. 2022, Zhang et al. 2025) including more recently one by our group (Dossa et al. 2025), little is known about the evolutionary biology of Dioscorea alata. Using GBS data and based on genetic parameters and demographic inference, evidence of early divergence of mainland Southeast Asian and Pacific gene pools was found, suggesting independent domestication origins (Sharif et al. 2020). However, with the advent of the new methods of sequencing and the availability of Telomere-to-Telomere genome references, the evolutionary history of greater yam needs to be investigated more deeply.

We have gathered accessions of Dioscorea alata from different geographical origins to build up a collection representative of the worldwide diversity. This panel represents approximately 199 accessions for which whole genome sequencing data are available.

Within this internship, the candidate will apply population genomic approaches to this worldwide sample in order to understand the demographic history of the species and to identify the genes under selection. Dioscorea alata is a polyploid species (2X, 3X and 4X). The accessions will be analyzed using multivariate approaches. The structure will be investigated to characterize the spatial distribution of genetic diversity and identify genetically different populations. Several genetic diversity statistics will be calculated for each population, to quantify the levels of nucleotide diversity and identify signatures of effective population changes (expansions or bottlenecks). Finally, using the annotated genome (Dossa et al. 2025) and the D. alata transcriptome, analyses will also be conducted to identify genes under selection between the different populations.