Rapid identification and interpretation of gene-environment associations using the new R.SamBada landscape genomics pipeline.
Lidia cattle breed
Moroccan sheep
gene-environment association
landscape genomics
local adaptation
r-package
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Sep 2019
Sep 2019
Historique:
received:
20
03
2019
revised:
10
05
2019
accepted:
13
05
2019
pubmed:
29
5
2019
medline:
18
1
2020
entrez:
29
5
2019
Statut:
ppublish
Résumé
samβada is a genome-environment association software, designed to search for signatures of local adaptation. However, pre- and postprocessing 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 samβada, 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 and 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 substructuring. 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).
Identifiants
pubmed: 31136078
doi: 10.1111/1755-0998.13044
pmc: PMC6790591
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1355-1365Subventions
Organisme : FACCE ERA-NET Plus
ID : ANR-14-JFAC-0002-01
Organisme : H2020 Marie Skłodowska-Curie Actions
ID : DLV-655100
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M019276/1
Pays : United Kingdom
Organisme : FP7 Food, Agriculture and Fisheries, Biotechnology
ID : 244356
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2019 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.
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