Tropentag, September 16 - 18, 2026, Göttingen "Towards multi-functional agro-ecosystems promoting climate-resilient futures"

Genomic diversity of Peruvian llamas: Population structure and SNP identification for resilient Andean livestock systems

¹Universidad Nacional Agraria La Molina, Facultad de Zootecnia, Peru
²Iowa State University, Dept. of Animal Science, United States

Abstract

The llama (Lama glama) is a key genetic resource in high-Andean ecosystems, exhibiting resilient adaptive biology in response to conditions of hypoxia, low-nutritional-value forage, water scarcity and high climatic variability. Despite its biological and socioeconomic importance, its genomic diversity and population structure remain insufficiently characterised. Therefore, this study aimed to identify single nucleotide polymorphisms (SNPs) and assess the population structure of llamas in Peru. A sample of 200 llamas from central and southern regions of Peru was used for SNP calling by genotyping-by-sequencing (GBS). A reduced representation library was prepared using double digestion of the DNA with the restriction enzymes PstI-MspI. Single-end sequencing (1×101 bp) generated an average of 4.2 million high-quality reads per sample. Sequence alignment was performed with the alpaca reference genome VicPac4 due to its genetic similarity to the llama, its chromosomal assembly, and its greater accuracy among South American camelids. A total of 412,459 SNPs were identified with a minimum quality score of 10, a genotyping rate ≥ 0.10, and a minor allele frequency ≥ 0.01. Of the SNPs identified, 97.97% are located on autosomes. The analysis of population structure using multivariate methods revealed clear genetic differentiation between populations from central and southern Peru. This elevated diversity may be explained by the presence of three phenotypic varieties, K’ara, Chaku and Intermedia, within the study areas. This study provides a comprehensive assessment of genomic diversity in Peruvian llamas, establishing a robust framework for characterising population structure and guiding resilient management and conservation strategies in Andean livestock systems.

Keywords: Genomic diversity, sequencing based genotyping, South American camelids

Contact Address: Eduardo Leuman Fuentes Navarro, Universidad Nacional Agraria La Molina, Facultad de Zootecnia, Jr. Camilo Carrillo 214 Dpto 502 Jesús María, Lima, Peru, e-mail: efuenteslamolina.edu.pe