Mots-Clés

WGS structural variations animal genetics and genomics bioinformatics

Description

YOUR MISSION AND YOUR ACTIVITIES

You will work in the Bovine Genetics and Genomics (G2B) team within the Animal Genetics and Integrative Biology unit (UMR-1313 GABI; https://www6.jouy.inrae.fr/gabi).
The G2B team brings together a wealth of expertise in genomic selection and in the analysis of genetic variability. Our research is focused on contributing to the sustainability of bovine production in its economic, social and environmental dimensions. These objectives leverage high-throughput genotyping and sequencing technologies, coupled with advances in bioinformatics.
The project aims at efficiently detecting and integrating structural variants (SVs), which are large genomic variations (> 50 nucleotides), into the bovine genome analysis in order to identify all genetic variants responsible for the variability of complex traits. The approach consists of combining data from two sequencing technologies: short reads produced for 6500 animals using Illumina NovaSeq technology and long reads for 163 individuals generated with PacBio CLR or HIFI technologies.

You will be more specifically in charge of:
     - Implementing novel approaches combining different types of genomic sequence data in order to improve the search for SVs.
     - Developing an efficient imputation method to accurately predict SV genotypes from microarray genotyping data for hundreds of thousands of individuals.
     - Exploring potential associations between SVs and phenotypes of interest, as well as possible genetic defects.
The results obtained in this project will help to better understand the determinism of Mendelian and complex traits in cattle and enhancing genetic improvement.

Special conditions of activity:
Bioinformatics analyses to study SVs from long sequences will be carried out in collaboration with Thomas Faraut from the Genetics Physiology and Livestock Systems unit (https://genphyse.toulouse.inra.fr/) and Christophe Klopp from the SIGENAE bioinformatics platform (https://www.sigenae.org/). Therefore short stays are planned at Toulouse INRAE center.

THE PROFILE WE ARE LOOKING FOR :
     - Recommended experience: PhD in bioinformatics 
     - Desired knowledge: animal genetics and genomics
     - Experience appreciated: bioinformatics analyses of high-throughput genomic sequences, quantitative genetics
     - Required skills: Strong interest in animal genetics and genomics, experience in programming (preferentially Python and R), and               - practical knowledge with computing clusters. Ability to write scientific articles and make oral communications. Good knowledge of English.