This repository contains data files and source code used in a project in which we looked for genome-wide association with high-resolution climate data of the Iberian Peninsula with the goal of discovering selection footprints in the genomes of barley landraces from the Spanish Barley Core Collection. The results of the project are summarized at https://doi.org/10.1111/mec.15009
URL: eead-csic-compbio.github.io/barley-agroclimatic-association
Authors
B Contreras-Moreira (1,2), R Serrano-Notivoli (1), NE Mohamed (1), CP Cantalapiedra (1), S Begueria (1), AM Casas (1), E Igartua (1)
- Estacion Experimental de Aula Dei-CSIC, Zaragoza, Spain
- Fundacion ARAID, Zaragoza, Spain
There are several R markdown documents describing the selection of agroclimatic variables, mapping and diverse protocols for association analyses:
| filename | summary |
|---|---|
| HOWTOclimate | Preparation and selection of climate variables |
| HOWTOstructure | Analysis of population structure of Spanish barleys |
| HOWTORDA | Redundancy Analysis |
| HOWTOLD | Linkage Disequilibrium |
| HOWTOsnps | Association between SNPs and climate variables (Bayenv2) |
| HOWTOsnpsLFMM | Association between SNPs and climate variables (LFMM) |
| HOWTOXtX | XtX subpopulation differentiation (Bayenv2) |
| HOWTOXtX_BAYPASS | XtX subpopulation differentiation (BayPass) |
Data files
The table below describes some data files used in this work. You can find them in the repository, mainly at maps/, and raw/ folders, if you click on View on GitHub:
| filename | description |
|---|---|
| raw/barley_climate_updated.tsv | Values of agro-climatic and environmental variables at the geographical collection points of the barley accessions. |
| raw/barley_climate_pca_scores.tsv | Values of principal components of the agro-climatic and environmental variables at the geographical collection points of the barley accessions. |
| maps/climatologies_5km.RData | 5x5 km grids of agro-climatic and environmental (lat, lon, alt) variables over Spain, required for producing the maps in HOWTOclimate. |
| maps/climatologies_5km_pca.RData | 5x5 km grids of principal components of the agro-climatic and environmental variables over Spain, required for producing the maps in HOWTOclimate |
| matrices/SBCCmatrix_nr_mean.txt | Non-redundant covariance matrix obtained by averaging 10 Bayenv2 replicates. |
| raw/SBCC_Kinship.full.tsv | Tab-separated file assigning SBCC landraces to 4 subpopulations. |
| raw/9920_SNPs_SBCC_50K.tsv | Tab-separated matrix with SBCC biallelic SNPs. |
| raw/9920_SNPs_SBCC_bp_map2017.curated.tsv | Tab-separated file with physical positions of SNPs assigned by BARLEYMAP |
| raw/9920_SNPs_SBCC_cM_map2017.curated.tsv | Tab-separated file with genetic positions of SNPs assigned by BARLEYMAP |
Bayenv demo
A demo dataset to learn how to run bayenv2 locally is available at bayenv/BAYENV_EXAMPLE.tgz.
It can be downloaded in the terminal with:
wget https://eead-csic-compbio.github.io/barley-agroclimatic-association/bayenv/BAYENV_EXAMPLE.tgz
Downloads
It is possible to get the complete dataset, source code and documentation in two ways:
- downloading the release (143MB)
- cloning the GitHub repository (783MB)
Dependencies
Besides bayenv2, LFMM and a few Perl scripts, included in this repository, these protocols require a few R packages which must be installed to reproduce the results:
LDcorSV, ape, calibrate, cluster, corrplot, dendextend, devtools, dplyr, ggplot2, gplots, grid, knitr. maptools, pracma, qqman, raster, vegan.
The BayPass XtX protocol requires the system installation of BayPass.