Genotyping by sequencing-based genetic insights into Argentine llama populations and breeding impacts

Llama breeding is an important source of economic income for Andean communities, thus ensuring llama biodiversity is fundamental to making breeding decisions that promote sustainable production. Despite this, there is limited information on the genetic diversity of llama populations in Argentina. Moreover, some llama herds in the northwest region of the country exhibit low reproductive efficiency and a high incidence of congenital abnormalities. In this study, we used genotyping by sequencing, a genome-wide approach, to estimate the genetic diversity of Argentine llama populations, assess their conservation status and inbreeding levels, and discuss the impacts on breeding. Overall, our results indicate that current llama populations in the northwest present moderate to high genetic diversity, although a recent reduction in population size was detected for two of them. Population structure was subtle, although three clusters, with some substructure, were recognized. The inbreeding coefficient values were similar for all populations showing moderate to high inbreeding levels. There was a predominance of short homozygous segments, which is indicative of ancient consanguinity. However, recent autozygosity events were evidenced in some llamas with congenital disorders. Thus, we investigated the chromosomal region to find potential candidate genes for such traits. The genes MYO15A and USH1G are proposed as candidates for pigmentation-associated deafness, although further research is needed. This study establishes an initial step towards understanding the genetic diversity of Argentine llamas, highlighting the necessity of reducing current inbreeding levels and implementing continuous monitoring to improve breeding decisions and support a sustainable production system for the species.