**********Genotype data_Ben_cattle_2016-2019***********
Description: 
2009_Afr_Dah_Cattle_f.bed (.bim, .fam) correspond to 50k SNP genotype data in .bed format (PLINK binary biallelic genotype table) after quality control in PLINK (Purcell et al., 2007)
The genotypes are from 430 Beninese cattle sampled in Benin and 30 Dahomey cattle sampled in four European countries (Germany, Austria, Switzerland, Czech Republic) for out study.
The "SampleInfos.txt" file contains different information (Sample.ID, Sample.Name, Breed, agro-ecological zones or country) of the animals.


Number of variants: 40,109 SNP 

Number of animals: 460 cattle

Breeds:
1)African taurines (AFT): 
Dahomey: 30; 
Lagune:  137
Somba: 58
2) African Hybrids
Borgou: 177
Pabli: 58


Analyses
We used this data to define main genetic clusters used as populations in this study (see Table). 
The unsupervised k-means clustering were applied with the “adegenet” software (Jombart, 2008; Jombart and Ahmed, 2011) and the dataset was first pruned for LD and converted in Structure format in PLINK (Purcell et al., 2007) as required by “adegenet”.
The dataset was also used to infer population structure with the Faststructure software (Raj et al., 2014).

Abbreviations in the SampleInfos.txt file

AEZ : agro-ecological zones
OA: Ouest Atacora
CNB: Cotonnière Nord Borgou 
CCB: Cotonnière Centre Borgou
VSB: Vivrière Sud Borgou 
CNB: Cotonnière Nord an
P: Pêcheries
D: Dépression
TB: Terre de Barre

Country:
AT: Austria
DE: Germany
CZ: Czech Republic
CH: Switzerland 

References:
Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405. doi: 10.1093/bioinformatics/btn129
Jombart, T., and Ahmed, I. (2011). adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071. doi: 10.1093/bioinformatics/btr521
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 81, 559–575.
Raj, A., Stephens, M., and Pritchard, J. K. (2014). fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573–589. doi: 10.1534/genetics.114.164350.