Master of Science, Universite Libre De Bruxelles (2010)
Bachelier, Universite Libre De Bruxelles (2008)
Doctor of Philosophy, Ecole Polytechnique Federale Lausanne (2015)
Rapid identification and interpretation of gene-environment associations using the new R.SamBada landscape genomics pipeline.
Molecular ecology resources
Sambetaada is a genome-environment association (GEA) software, designed to search for signatures of local adaptation. However, pre- and post-processing of data can be labour-intensive, preventing wider uptake of the method. We have now developed R.SamBada, an R-package providing a pipeline for landscape genomic analysis based on Sambetaada, spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline, eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure, and Lidia cattle from Spain displaying population sub-structuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the R CRAN package repository and on GitHub (github. com/SolangeD/R.SamBada). This article is protected by copyright. All rights reserved.
View details for DOI 10.1111/1755-0998.13044
View details for PubMedID 31136078