DOI: 10.5061/dryad.z8w9ghxmx
title: SNP data set of the Peruvian Creole cattle from southern Peru

description: 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, possibly due
 to admixture. The lowest FST (0.005) was estimated for Ayacucho and Cusco
 cattle populations, and the highest FST (0.028) was reported for Puno and
 Apurimac cattle population. Small genetic variation among populations
 (3.65%) but higher variation within populations was found using AMOVA. To
 the best of our knowledge, this is the first study employing SNP markers
 in PCC, and as such it is hoped that this helps to pave the way towards
 its genetic improvement and the urgent sustainable management of creole
 animals in Peru.
description: # 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. Then, 5732 SNPs and five Creole individuals were removed due to low
 call rate and minor allele frequency (MAF); and low genotyping,
 respectively. As a last step, linkage disequilibrium pruning was
 performed. Finally, a set of 24200 SNPs and 69 Creole individuals from
 Cusco (n=17), Apurimac (n=18), Puno (n=23) and Ayacucho (n=11) were
 retained. References: 1.  Sempéré, G., Moazami-Goudarzi, K., Eggen, A.,
 Laloë, D., Gautier, M., & Flori L. WIDDE: a Web-Interfaced next
 generation Database for genetic Diversity Exploration, with a first
 application in cattle, BMC Genomics. 2015, 16:940. 2. Purcell, S., Neale,
 B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller,
 J., Sklar, P. de Bakker, P. I. W., Daly, M. J. & Sham, P. C. (2007).
 PLINK: A tool set for whole-genome association and population-based
 linkage analyses. Am. J. Hum. Genet. 81, 559–575. doi:10.1086/519795.