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, 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.