***********Genotype data_extended 1***********
Description: 
2009_Ben_breed_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 dataset contains Beninese indigenous cattle genotypes including own data (current) and historical data retrieved from the WIDDE database (Sempéré et al., 2015). 

Number of variants: 32,533 SNP 

Number of animals: 586 cattle

Breeds:
1)African taurines (AFT): 
Dahomey: DAH_cur (30); 
Lagune: LA_cur (110); LA_out(25); LA_hist (44); 
Somba: SO_cur (57); SO_hist (44); 
2) African Hybrids
BO_cur (135); Adm_cur (98); BO_hist (45).


Analyses
This dataset was used to perform diversity analyses (principal component analysis, unsupervised k-means clustering), estimation of inbreeding coefficients and selection signatures.
For the unsupervised k-means clustering with the “adegenet” software (Jombart, 2008; Jombart and Ahmed, 2011), the dataset was pruned for LD and converted in Structure format in PLINK (Purcell et al., 2007) as required by “adegenet”.
For the selection signature analyses, this dataset was phased and missing variants were imputed in Beagle 5.1 (Browning et al., 2018).

References:
Bertrand, A. R., Kadri, N. K., Flori, L., Gautier, M., and Druet, T. (2019). RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous‐by‐descent segments. Methods Ecol Evol 10, 860–866. doi: 10.1111/2041-210X.13167
Browning, B. L., Zhou, Y., and Browning, S. R. (2018). A One-Penny Imputed Genome from Next-Generation Reference Panels. Am J Hum Genet 103, 338–348. doi: 10.1016/j.ajhg.2018.07.015
Druet, T., and Gautier, M. (2017). A model-based approach to characterize individual inbreeding at both global and local genomic scales. Mol Ecol 26, 5820–5841. doi: 10.1111/mec.14324
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.
Sempéré, G., Moazami-Goudarzi, K., Eggen, A., Laloë, D., Gautier, M., and Flori, L. (2015). WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle. BMC Genomics 16, 940. doi: 10.1186/s12864-015-2181-1