Rapid identification and interpretation of geneāenvironment associations using the new R.SamBada landscape genomics pipeline
SamĪ²ada is a genomeāenvironment association (GEA) software, designed to search for signatures of local adaptation. However, preā and postāprocessing of data can be labourāintensive, preventing wider uptake of the method. We have now developed R.SamBada, an Rāpackage providing a pipeline for landscape genomic analysis based on SamĪ²ada, 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 subāstructuring. 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
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