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 (F_IS) values for PCC from Puno and Ayacucho were also found, possibly due to admixture. The lowest F_ST (0.005) was estimated for Ayacucho and Cusco cattle populations, and the highest F_ST (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.