Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

SIMPLE SUMMARY: Alpacas (Vicugna pacos) are South American members of the tribe Lamini of the Camelidae family. They are bred for their fiber, which is considered a luxury material. Interest in alpaca breeding is increasing in Poland, but the local alpaca population is relatively young and heterogeneous. The poor quality of alpaca fiber results from uncontrolled crossing with llamas (Lama glama). Hybridization between the two species is a well-known phenomenon among alpaca breeders worldwide and is the cause of poor fiber quality, which leads to economic losses. Microsatellite markers can distinguish alpacas from llamas and indicate the level of admixture. However, it is difficult to determine in which generation the admixture took place. The high genetic diversity of alpacas bred in Poland has emerged as a consequence of their mixed origins. In this context, the microsatellite markers recommended by the International Society for Animal Genetics have been shown to be highly useful for individual identification and parentage testing of alpacas. ABSTRACT: This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.