Internship OT-27868
Stage-Master 2-Constructing Connected High-Resolution Genetic Maps in pepper
84140 Montfavet
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
Keywords – SNP calling, genetic map, QTL, candidate genes, disease resistance, agronomic traits, Capsicum annuum
Background – Reducing pesticide use in crop systems relies heavily on growing disease-resistant plants, but traditional breeding to transfer resistance traits into new cultivars is a time-consuming process, especially when considering several pathogens. Moreover, many major resistance genes often become ineffective against evolved pathogen variants. By contrast, quantitative resistance—governed by multiple loci or QTLs (Quantitative Trait Loci)— has proved to offer generally more durable plant health.
Pepper (Capsicum annuum L.), cultivated worldwide, faces threats from a wide array of pests and pathogens. While several genetic maps and QTLs related to disease resistance in peppers have been published, recent advances in genotyping now enable the development of high-density genetic maps from larger progenies, facilitating the identification of a short list of candidate genes for quantitative resistance. Our current projects aim to leverage these technological advancements to enhance breeding for multi-disease resistance in pepper.
Internship Overview – A genotype–phenotype association identified in genome-wide association studies (GWAS) links specific genetic variants to observable traits in unrelated plant accessions. However, these statistical associations often require validation to confirm their causal relationships. Analysing biparental progenies enables such validation, as the controlled genetic background enhances the detection and strength of the observed effects.
Internship Objectives – The intern’s goal will be to develop three connected high-resolution genetic maps based on large biparental pepper progenies, aligned with a common reference genome.
The intern will:
- perform the SNP (single nucleotide polymorphism) calling from sequencing datasets of three pepper progenies and establish a catalogue of SNPs anchored to a common reference genome,
- construct three high-resolution genetic maps anchored to each other’s,
- format historical phenotypic datasets according to FAIR (Findable, Accessible, Interoperable, Reusable) data principles,
- format and store genotypic and phenotypic datasets into the Thaliadb database,
- perform QTL (quantitative trait locus) and GWA (Genome Wide Association) studies,
- establish an analytical pipeline that can be reused by the research team,
- compare the QTL positions among the 3 genetic maps with the GWAS results (McLeod et al. 2023) to refine the SNP-phenotype links.
These results should provide a solid basis for validating genetic effect of SNPs on phenotypes, thereby facilitating more efficient pepper breeding.
Throughout, the intern will align with INRAE’s open science policy, ensuring that data and code adhere to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) and are stored in appropriate repositories.
Main Activities – Bioinformatics, Mendelian and quantitative genetics, Data management, Application of FAIR principles, Data interpretation, Reporting.
Training and skills
Experience Acquired During the Internship – Proficiency in R and statistical analysis; Experience in Linux and bioinformatics tools; Facilities in FAIR Principles, data management and R script editing; Ability to understand scientific literature; Scientific writing and oral communication skills.
Language Spoken: French for daily interactions, English used as needed for non-French-speaking interns.
Candidate Profile – A keen interest in plant genetics and management of large datasets; Solid understanding of statistical methods and data analysis; Experience in R programming and Linux; Interest in scientific literature, Problem-solving, Teamwork & communication; Proactive approach; Intellectual curiosity; Commitment to research excellence.
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- up to 30 days of annual leave
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- sports and cultural activities;
- collective catering.
How to apply
I send my CV and my motivation letter
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, 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. > Find out more: fonction publique.gouv.fr website (in French)