Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes

Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.