Genomic Tools for South American Camelids: Genotyping-by-Sequencing Is a Cost-Effective Tool for Alpaca Breeders in Peru

Peruvian alpacas represent 85% of the global population and are mainly bred for their fiber and adaptation to high-altitude Andean environments. Two distinct phenotypes exist: Huacaya and Suri. This study aimed to investigate the genetic population structure of alpacas (Vicugna pacos) using genotyping by sequencing (GBS), also known as restriction enzyme-reduced representation sequencing, and to evaluate its application as a breeding tool. We sampled 838 Huacaya and Suri alpacas of varying coat colors and fiber qualities from ten locations in Cusco and Puno, Peru. After quality filtering, 68,641 high-confidence SNPs were obtained. These were used to estimate inbreeding, population differentiation (Fst), and observed and expected heterozygosity. Mean values of inbreeding, observed heterozygosity, and expected heterozygosity were 0.05, 0.30, and 0.34, respectively. Several animals across all sampling sites exhibited high inbreeding levels (≥0.20). Low genetic differentiation between Huacaya and Suri suggested close genetic relationships and continuous gene flow despite marked phenotypic differences. Overall, the results demonstrate that GBS provides a powerful and cost-effective approach for SNP discovery and genotyping in alpacas, offering valuable insights for genomic characterization and the potential identification of markers associated with productive traits in South American camelids managed by smallholder breeders.