SNP data set of the Peruvian Creole cattle from southern Peru

The Peruvian creole cattle (PCC) was originated after the introduction of cattle into the American continent about five centuries ago, and is an important source of power for agriculture, meat, and milk in the Peruvian highlands, as well as part of cultural traditions. However, little is known about the genetics of the PCC. In order to determine the genetic diversity and structure of the PCC, 69 DNA samples from four southern regions of Peru (Apurimac, Ayacucho, Cusco and Puno) were genotyped using a 100K SNP bead chip. After quality control and LD pruning, 24,200 SNPs were retained for further analysis. Animals were grouped into two clusters (C1: Apurimac, Ayacucho and Cusco, C2: Puno) using principal component analysis and UPGMA dendrogram. STRUCTURE analysis showed that individuals from Puno grouped in one cluster. Expected heterozygosity ranged from 0.399 (Apurimac) to 0.418 (Ayacucho). Negative inbreeding coefficient (FIS) values for PCC from Puno and Ayacucho were also found, poss..., , , # SNP data set of the Peruvian Creole cattle from southern Peru

We submitted our raw data (\"Peruvian Creole cattle_Figueroa et al.vcf\") 

Hair samples of the 74 individuals were genotyped using the Illumina GGP Bovine 100K SNP array by a commercial genotyping service provider, following standard procedures of the manufacturer. SNPs quality control was performed using PLINK v1.9 (Purcell et al., 2007). Only SNPs located on autosomes and with known genomic positions were considered for analysis. Individuals with missing genotypes in more than 10%, SNPs with missing rate higher than 10%, and minor allele frequency (MAF) lower than 0.05 were excluded. Additionally, for diversity and population structure analysis linkage disequilibrium pruning was done, using the PLINK parameter --indep 50 5 2.

From an initial set of 95,256 SNPs and 74 Creole individuals, quality control started by removing SNPs assigned to sex chromosomes and those without genomic locations where 90349 SNPs were left. The...