PhD project: Pangenome and structural diversity of the grapevine genome: Impact on grapevine vulnerability and adaptation to climate change:

Summary of thesis project: As they face climate change, new grapevines varieties will have to display adequate plasticity in the expression of their phenotypes.

Their selection requires thus a better knowledge of the genetic basis of this trait. Since they can be accumulated and fixed during clonal selection, the extent and impact of structural variations and chromosomal rearrangements in the rapid adaptation capacity of plants are of particular interest for vegetatively propagated perennial species.

With recent advances in long range sequencing techniques, these variations become prime study objects to characterize the genetic determinism of grapevine adaptation potential.

This thesis project is part of the ‘PlastiVigne’ project, an emblematic project of the Vinid’Occ key challenge, financed by the Occitanie Region, and coordinated by the host group. It is in line with INRAE’s major scientific objective 1 (GOS1): To manage, describe and analyze genetic and epigenetic diversity to understand the functioning and adaptation of plants and plant communities.

The thesis aims to:

i) Create a graph-pangenome on grapevine, using the already available high-quality genomes and a dozen of newly (large range) sequenced “cluster head” genomes, annotated in order to characterize conserved regions, more variable parts and “private” genes, regions of transposable element activity and variations in methylation profiles.

ii) Use this graph to genotype, from short fragments (Illumina) genomic sequences generated by the project, a diversity panel (279 genotypes) used for association genetics studies, as well as an already sequenced core collection (C4) of 200 varieties maximizing diversity on adaptive traits such as phenology or a latitude gradient; such genotyping will be used to identify signatures of adaptive selection.

iii) Genotype in the same way about 50 accessions of the wild subspecies Vi#s vinifera subsp. sylvestris, providing important information on grapevine adaptive evolution and domestication.

This pangenomics approach aims to answer the following questions:

  • How large is the part of the genome shared by all individuals and how much “private content ” is there within the pangenome?
  • What are the characteristics of structural variations and what could be their impact on grapevine adaptive plasticity?
  • Do gene duplications or changes in their methylation profile affect particular genes of interest for adaptation?
  • What is the contribution of transposable elements to this structural variation and the frequency of deleterious effects induced by their insertion in important genes?
  • Can the domestication and adaptation of grapevines on given terroirs be taken into account to identify key structural variations and explain vine adaptive plasticity?
  • Can we exploit these dynamics to create grape varieties with increased plasticity in face of environmental stress?

Keywords: Grapevine; pangenome; adaptation; evolution; climate change; structural diversity

Source of funding, employer

INRAE (Plastivigne project and BAP department)

Thesis director

Prof. THIS Dominique, Institut Agro Montpellier (, Tel +33-467615829


SARAH Gautier, INRAE ( BACILIERI Roberto, INRAE ( PIRELLO Julien, INP Purpan ( )  Doctoral School GAIA (University of Montpellier) Research Unit and Research team


AGAP Institute. Avenue d’Agropolis, Montpellier, France, DAAV team (Diversité, adaptation et amélioration de la vigne), PhD start 01/10/2023 Deadline for application (CV and motivation letter sent to ) 16/05/2023

The successful candidate should have a Master’s degree in plant genetics or bioinformatics and have strong experience in the analysis of large sequencing datasets, comparative genomics and be familiar with the LINUX environment.

The candidate must have good writing skills and a good mastery of spoken and written English and French (B2 level). Knowledge of one of the following programming languages: Bash/Python/Perl or R would be an asset.

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