Synbreed Biodiversity Panel Genotypes

Synbreed Diversity Panel Genotypes

These data have been made available coupled with the publication of Beissinger, T., Gholami, M., Erbe, M., Weigend, S., Weigend, A., de Leon, N., Gianola, D., and Simianer, H., Using the Varibility of Linkage Disequilibrium Between Populations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens, Heredity, 2015.

 

Please cite upon use.

 

Synbreed – Synergistic Plant and Animal Breeding (Synbreed) was funded by the German Federal Ministry of Education and Research (BMBF) from 2009 -
2014 (Funding ID: 0315526) ; web address http://www.synbreed.tum.de/

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Samples were genotyped with 580K SNP Affymetrix Axiom® Genome-Wide Chicken Genotyping Array.

 

Genotype_Matrix.Robj
This file is a matrix of genotypes from 1,417 chickens encompassing 72 breeds, genotyped as part of the Synbreed Project. The file can be loaded into R with the load() command. Individuals are in rows and marker genotypes, coded 0, 1, and 2, are in columns. Row names are a breed index, so all rows named "1" are from breed 1, all rows named "2" are from breed 2, and so on. Column names are marker names.

Genotype_Map.Robj
This file is a map describing the 564,939 markers that were genotyped. The file can be loaded into R with the load() command. Each row describes a marker. The first column, named "SNP" provides the marker name. This column corresponds to the rows of the Genotype_Matrix.Robj file. The second column, named "Chr", is the chromosome. The third column, named "Pos", is the physical position of the marker.