Résumé
Marginal land is land that is of little agricultural value because crops produced there would be worth less than any rent paid for access to the area. Helping to develop such zones in Africa is a key goal for the EU-funded EWA-BELT project. The aim is to promote the sustainable intensification of agricultural production in organic, agroforestry and mixed crop and livestock farming systems in 38 study areas of six countries belonging to East and West Africa. The project will enhance current scientific knowledge on the adaptation of new and improved traditional crops in different agroecosystems and the impacts of traditional agricultural practices on soil health. This initiation to genomic data analysis with R was designed within the EWA-BELT H2020 EU project (grant agreement ID 862848). The training module introduced to a variety of population genomics analyses for genotyping by sequencing (GBS) datasets. It included an introduction to single-nucleotide polymorphism (SNP) calling and filtering options, experimental design and various applications, population genomics statistics (genetic diversity and structure, Fst-based analyses) and genome-wide association studies (GWAS). The majority of the course consisted of practical R sessions to give hands-on experience of these analyses. Main topic and contents treated during the courses : Session 1. Passport data and Bioinformatics analysis Session 2. VCF filtering Session 3. Genetic diversity and structure Session 4. Genome-Wide Association Studies (GWAS) Each session includes a short introduction outlining the core concepts (PDF), R scripts (HTLM/PDF) and associated datasets.