Mots-Clés
Population genetics
Tuber crops
Cassava
Description
Cassava is monoecious shrub belonging to the Euphorbiaceae family. It is cultivated in tropical and sub-
tropical areas mainly for its starchy roots. It is the second most cultivated root and tuber crops, after
potato (FAO 2025), and is estimated to contribute to the diets of approximately 600 million to 1 billion
people worldwide (Parmar, Sturm, et Hensel 2017).
Cassava was domesticated in South America, most likely in the southern Amazon basin (Olsen et Schaal
1999; Watling et al. 2018). This region contains the greatest genetic diversity of cultivated cassava
(Ferguson et al. 2019). Cassava was later introduced to Africa and Asia (Ceballos et Fenstemaker 2026).
Genetic research on cassava has expanded with the increasing accessibility of sequencing technologies.
Since 2016, cassava has had a reference genome assembly based on the Colombian inbred line
“AM560-2”, which has been updated several times (Bredeson et al. 2016). This reference genome has
since been complemented by other genome assemblies. In addition, resequencing approaches have
been used to improve our knowledge on the intraspecific diversity, with the most comprehensive study
to date including approximatively one thousand individuals (Zhao et al. 2026). However, although
cassava diversity has been extensively studied, most of sequencing effort have been concentrated in
Colombia, Brazil, China and Nigeria.
Within ROTATES project (www.rotates.eu) we aim to sustainably enhance agrobiodiversity and
ecosystem services by introducing and promoting starchy root and tuber crops, including cassava, in
Europe, where they are currently considered as minor crops and underutilised despite increasing
consumer demand. We collected and conducted a whole genome short read sequencing of 178
accessions from understudied areas, namely French Guiana, Republic of Congo and Guadeloupe.
Despite its importance in French Guiana, representing the centre of origin and the Republic of Congo,
representing the African genepool, the cassava diversity and genetic origin have never been
investigated in these two countries.
Objectifs du stage :
The objective of the internship is to assess the genetic diversity of ROTATES cassava accessions,
especially to understand the cassava diversity in French Guiana and Republic of Congo in comparison
with a worldwide collection including more than 1000 accessions from the four continents and infer
their geographical origin.
Unité Mixte de Recherche Amélioration Génétique des Plantes méditerranéennes et tropicales (AGAP)
Avenue Agropolis – TA A-108/03 – 34398 Montpellier cedex 5 – France.
Courriel : diragap@cirad.fr – Site internet : http/umr-agap.cirad.fr
Programme du stage :
The inter will map WGS short-reads to the AM560-2 reference followed by variant calling to identify
single-nucleotide polymorphisms (SNPs). The resulting dataset will undergo quality control, filtering
and pruning will be performed to generate the appropriate datasets for downstream analyses.
Then, the intern will characterize the genetic diversity of the ROTATES panel in comparison the one
thousand accessions available using phylogeny reconstruction and other genome-based metrics such
as nucleotide diversity, heterozygosity and allele frequency. Population structure will be investigated
using principal component analysis (PCA), clustering approaches such as ADMIXTURE, and
phylogenetic reconstruction.
Finally, genomic results will be integrated with the available geographical and biological metadata. This
will allow the relationship between genetic variation, population structure and geographical origin to
be investigated, including potential patterns of geographic differentiation and isolation by distance.
Compétences requises :
• Competence and interest in scripting languages (Bash, Perl, and/or Python).
• Basic knowledge of NGS sequence data analysis methods.
• Good background in biological research, especially in population genomics and phylogenetics.