Société Française de Bioinformatique

Mots-Clés

Cattle Genetics & genomics bioinformatics WGS genetic variants selection signature

Description

YOUR MISSION AND YOUR ACTIVITIES

• You will be welcomed into the GBoS team (Genetics for Bovine Sustainability) within the Animal Genetics and Integrative Biology unit (UMR-1313 GABI ; https://www6.jouy.inrae.fr/gabi) and into the CHAMADE team (Characterization and Management of Genetic Diversity) within the Genetics, Physiology, and Breeding Systems unit (GenPhySE; https://genphyse.toulouse.inra.fr/). The thesis will be supervised by Mekki Boussaha and Aurélien Capitan, with co-supervision provided by Pascal Croiseau and Pierre Faux.

• The research conducted by the CHAMADE team facilitates the understanding and modeling of genetic diversity, its contribution to phenotypic variability, and its impact on the response to selection in livestock animals.

• The GBoS team is conducting its research focused on analyzing genetic variability and its implications for genomic selection. The objective of these studies is to enhance the sustainability of cattle production across its economic, social, and environmental aspects. The research primarily relies on high-throughput sequencing and a whole genome sequencing (WGS) database encompassing 1381 animals from 31 French cattle breeds (RBF). This proprietary database is consistently updated with genomes generated from various projects. Within a year, it is anticipated that around 500 new genomes, including approximately fifty from at least five additional French local breeds with distinctive traits, will be incorporated. Furthermore, the team has access to sequencing data from 6271 cattle provided by the international consortium 1000 Bull Genomes (comprising 5206 Bos taurus, 985 Bos indicus, and 80 ‘Outspecies’ such as bison, yaks, etc.). This framework has facilitated the discovery of over 151 million genetic variants, including SNP (single nucleotide polymorphism) and InDel (small insertion & deletion) types, which are uniformly distributed throughout the bovine genome. This exceptional and comprehensive database serves as a highly effective tool for precisely mapping genomic regions influenced by selection pressures. By analyzing these regions across different breeds, we will possess the requisite capability to pinpoint potentially causal mutations. Subsequently, we will be able to characterize the impact of specific causal variants that are fixed in certain breeds by leveraging the breeds in which they continue to segregate, in conjunction with the extensive datasets of pedigree, SNP chip genotype, and performance data routinely collected in France for selection and population management.

• In this thesis project, the objective is to leverage the high-density genomic datasets available for French cattle breeds to tackle several important scientific inquiries at the crossroads of population genetics, functional genomics, and bioinformatics:

  1. What is the genetic structure of French cattle breeds?
  2. The doctoral candidate will concentrate on delineating the population structure, phylogenetic connections among breeds, as well as the historical and contemporary admixture events that have influenced their present diversity.
  3. Which genomic regions exhibit evidence of artificial or natural selection?
  4. By employing selection signature methodologies, the aim will be to pinpoint the genomic regions that have experienced selective pressures across approximately thirty French breeds and to analyze their profiles.
  5. What potentially causal genetic variants have been favored, and what traits do they affect ?
  6. The doctoral candidate will endeavor to isolate candidate variants within the identified regions, predicting or assessing their impacts on traits of interest (such as milk production, morphological traits, and adaptation), utilizing phenotype data, SNP chip genotypes, WGS sequences, and pedigrees.
  7. How can this knowledge be applied for selection and traceability purposes?
  8. A crucial component of the work will involve facilitating the technological transfer of findings through the creation of marker panels that can be employed for :
     • breed assignment,
     • origin verification of products under designation (AOP, IGP),
     • targeted selection or introgression of variants of interest.

*You will hold specific responsibilities for :*
- Analyzing the demographic composition and examining the phylogenetic connections among French cattle breeds, including both ancient and contemporary admixture events;
- Detecting selection signatures in around thirty French cattle breeds;
- Identifying causal variants within genomic regions that are under selection pressure and evaluating their influence on relevant phenotypes (data pertaining to milk production, evidence of selection, morphological traits, etc.).

• The proposed thesis project aims to emphasize the genetic variants that contribute to the diversity, robustness, and distinctiveness of French cattle breeds, outline their effects on various traits, and promote their application for selection, conservation, or enhancement of products.

• The doctoral candidate will carry out his/her thesis at the Jouy-en-Josas INRAe research center, participating in regular discussions with the GenPhySE unit in Toulouse. To support this collaboration, video conferences will be scheduled biweekly with the doctoral candidate and their co-supervisors. Project collaborators will consistently join these meetings depending on the thesis’s progress. Furthermore, the doctoral candidate will make several trips to Toulouse for visits that may range from one to two weeks, contingent upon the project’s needs.

• The bioinformatics tools designated for the study are available through the genotoul-bioinfo platform. The pipelines created during the thesis will be promptly accessible on the genotoul-bioinfo platform and will be applicable for the analysis of genomes from various species, thereby significantly broadening the influence of the project’s outcomes.

Specific activity conditions :
Anticipate some travel and short stays between the two INRAE centers located in Jouy-en-Josas and Toulouse.

THE PROFILE WE ARE LOOKING FOR
* Recommended qualification : Master’s degree or equivalent (Bac +5) in bioinformatics
* Desired knowledge: genetics and genomics in eukaryotes
* Preferred experience: bioinformatics analysis of high-throughput genomic sequences
* Required skills: A strong interest in animal genetics and genomics, experience in programming (in Python and R), practical knowledge of computing clusters, ability to write scientific articles and communicate orally. Proficiency in English is required

YOUR QUALITY OF LIFE AT INRAE
By joining INRAE, you will be able to benefit, depending on the type of contract:
* up to 30 days off + 15 RTT per year (for full-time)
* parenting support: CESU childcare, leisure services;
* skills development schemes: training, career guidance advice;
* 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.