Exploring the genomic diversity of native Peruvian guinea pigs (Cavia porcellus) from high Andean areas, a vision for the conservation of animal genetic resources in Peru

Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite their economic and cultural relevance, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from 6 regions of the Peruvian Andes and 1 group of improved animals. The paired-end (2 x 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample.