OPEN COMPETITIONS CR-2024-BAP-1
Junior Research Scientist in structural genomics for the study of the genetic diversity of the vine
34398 MONTPELLIER
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INRAE presentation
The French National Research Institute for Agriculture, Food, and the Environment (INRAE) is a public research establishment under the dual authority of the Ministry of Agriculture and the Ministry of Research.
INRAE is recruiting researchers by open competition and offering permanent position.
It is a major player in research and innovation created on 1st of January 2020. INRAE is a research institute resulting from the merger of INRA and IRSTEA. It is a community of 12,000 people with more than 200 research units and 42 experimental units located throughout France.
The institute is among the world leaders in agricultural and food sciences, in plant and animal sciences, and is 11th in the world in ecology and environment. INRAE’s main goal is to be a key player in the transitions necessary to address major global challenges. In the face of the increase in population, climate change, scarcity of resources and decline in biodiversity, the institute develops solutions for multiperformance agriculture, high quality food and sustainable management of resources and ecosystems.
Work environment, missions and activities
Environment:
The Research Associate will join the DAAV team (DIversity, adaptation and Breeding of grapevine; 11 scientists and 7 technical staff) and the UMT GenoVigne within the UMR AGAP (300 permanent staff including 180 researchers). Activities will be carried out in synergy with AGAP's bioanalysis platform and in conjunction with the Southgreen platform (https://www.southgreen.fr/).
At the heart of the fine analysis of the grapevine pangenome, the researcher will interact with colleagues from the CRB Vigne, scientists involved in studying the genetic bases of traits of interest, scientists involved in physiology and functional genomics and genomic prediction, from DAAV and other teams in the Vigne BAP group.
Mission:
The researcher will develop a research project aimed at identifying genome-wide polymorphisms to define the Vitis vinifera 'Pangenome', i.e. identify genes belonging to the 'cloud & shell' parts of the pangenome, enriched for 'beneficial' functions (defence, development, adaptation; Gordon et al, 2017), genes linked to abiotic stresses and controlling flowering (Tranchant-Dubreuil et al, 2019), or participating in specific metabolic pathways (example / soya: fatty acid biosynthesis; Liu et al, 2020) and their diversity. Particular attention will also be paid to 'Presence-Absence' (PAV) and 'Copy Number Variation' (CNV) polymorphisms, which have been an important source of variation during domestication (Lye & Purugganan, 2019, Zhou et al 2019) and mobile elements (transposons and retroelements) and their impact on adaptation and resilience.
Activities
Work will start on the database of complete sequences (haplotypic assembly) of genomes available in the team (Cabernet Franc, Chenin, Madeleine Noire des Charentes, Merlot, Pinot) and data available in international databases. We will then consider Pacbio deep sequencing of Vitis vinifera core-collections (panel 279, core C4) chosen for their strong environmental gradient or for which precise phenotypic data will be available, either as part of the CRB Vigne or current (G2WAS) or future research projects (implementation of panel 279 on the Pech Rouge experimental estate).
In conjunction with other researchers in the team, and thanks in particular to the phenotypic data accumulated at the Vassal estate, it will be possible to look for correlations between polymorphisms in the whole genome or in candidate genes and the traits impacted by climate change (1st trait worked on = phenology, quality). The phenotypic data that will be collected on the 279 panel in the field with repetitions and differentiated water treatment will also be very interesting for this objective.
The study of genetic diversity at this fine scale will also make it possible to identify potential targets for functional validation by editing and will shed light on breeding programmes and genomic prediction tools by taking better account, in addition to SNP diversity, of other types of genome variation: PAV, CNV, transposable elements. The study of epigenetic markers (small RNAs, methylation, etc.) could also be carried out in collaboration with other AGAP teams and the vine group.
Driving license recommended
Training and skills
Open to applicants with a PhD (or equivalent).
The competition is open to candidates with a PhD (or equivalent) in structural genomics, with skills in genomics and population genetics and solid bioinformatics skills. Good knowledge of statistics, particularly Bayesian statistics, programming concepts and R software is also required. Previous knowledge of vine diversity (ampelography) would be a plus.
INRAE's life quality
By joining our teams, you benefit from:
- 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.
For international scientists: please visit your guide to facilitate your arrival and stay at INRAE.
All persons employed by or hosted at INRAE, a public research establishment, are subject to its internal regulations, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear.