Mots-Clés
Population genetics
pangenome
Root and Tuber crops
Taro
Description
Title : Benchmarking graph-based and linear-reference approaches for population-scale variant
discovery in orphan crop: case study of taro (Colocasia esculenta L. (Schott))
Contexte :
Taro is a starchy vegetatively propagated crop, widely cultivated in tropical and sub-tropical areas. It
is also grown in temperate regions. Taro plays an essential role for food security and is often cultivated
in backyards or home gardens. Consequently, there is an underestimation of its production as many
countries does not report the statistics of their own production (Lebot et al. 2022).
The geographic origin of taro domestication is still unresolved. Molecular analyses indicate the
presence of two separate gene pools located in the Asia-Pacific region and India (Lebot and Aradhya
1991, Chaïr et al. 2016). From there the species likely spread to Africa and Americas. Taro has a basic
chromosome number of n = 14, with diploids (2n = 28) or triploids (3n = 42) forms (Coates et al. 1988,
Wang et al. 2017).
Despite its importance, taro research has been overlooked up to now, and limited genomic resources
are available. Recently, two genome assemblies at chromosome level have been produced, the
Chinese landrace “Lipu taro aka Bun Long” (Sun et al. 2026) and ‘Longxiangyu’, a widely cultivated
landrace in Jiangsu, China (Yin et al. 2020). The haploid taro assembly was around 2.45 Gb total with
repeat content of 82% (Bellinger et al. 2020). Two additional genome assemblies originating from
Hawaï “Moi” and “Niu” varieties are assembled at scaffold level only. Additionally, some population
diversity datasets are available based on Genotyping by Sequencing or microsatellite (SSRs) markers.
This reduced knowledge on taro genome and genetic resources hampers the studies of its evolutionary
history, domestication and deciphering its genetic architecture.
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 taro, in
Europe, where they are currently considered as minor crops and underutilised despite increasing
consumer demand. Thus, we collected 58 accessions from five partners and 13 countries, from Asia,
Pacific, Europe and Americas. To assess their genetic diversity, we conducted a whole genome short
read sequencing. As two reference genome assemblies are available and the genetic relationship
between the ROTATES samples and those two references is unknown, the prerequisite is to identify
the best strategy to capture the full range of genomic variations among the collected ROTATES
samples.
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
Objectifs du stage :
Therefore, the objective of this internship is to identify if calling variants on different references has
an impact in the reconstruction of the genetic relationship among ROTATES taro varieties.
Furthermore, the internship aims to categorize large structural variations and their use to infer taro
population structure.
Programme du stage :
The intern will, hence, i- reconstruct and compare ROTATES taro varieties genetic relationship, by
mapping ROTATES WGS short-reads onto the two genome assemblies and on a two-graph based
reference, and ii- categorize structural variations among genome references, using a syntenic
approach, and iii-analyse their impact on structuring taro populations.
To identify the impact of reference genome and structural variations on population genetic analyses,
you will:
i- compare the mapping parameters (percentage of reads mapped, properly paired reads,
mapping quality, uniquely mapped reads, coverage, coverage uniformity, number of
poorly mapped regions), the variants discovery (SNPs, small indels, presence/absence
variation, structural variants), and population genetic statistics (number of segregating
variants, allele frequency spectrum, missing genotypes, heterozygosity, nucleotide
diversity, population structure) obtained from the different taro genome references.
ii- Evaluate the potential of structural variants as markers for population genetic analyses by
assessing their ability to discriminate among taro genomes and to resolve population
structure and phylogenetic relationships based on their presence/absence patterns
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.
Indemnisation et avantages proposés : 654,73 euros par mois (au prorata du nombre d’heures
travaillées par mois)
Dates et lieu de stage : Stage de 6 mois à partir de janvier 2027 – CIRAD, UMR AGAP Institut.