Genetic Characterization of Huacaya Alpacas (Vicugna pacos) in Poland Using Microsatellite Markers

Alpacas (Vicugna pacos) are of increasing economic importance, mainly due to their high-quality fiber. This study aimed to develop and validate molecular tools for sex identification, individual identification and parentage testing, and to characterize genetic diversity and population structure in Huacaya alpacas bred in Poland. Forty-five previously described microsatellites and one newly developed SRY-based marker were organized into three multiplex panels containing sixteen, seventeen and thirteen markers. The SRY marker was validated in 17 reference animals of known sex (5 males, 12 females) and subsequently in 239 study animals, showing complete concordance with recorded sex. The 44 microsatellites, excluding SRY and the monomorphic YWLL02, showed a mean of 11.45 alleles per locus, observed heterozygosity (Ho) of 0.708, expected heterozygosity (He) of 0.755 and mean polymorphism information content (PIC) of 0.727. Combined non-exclusion probabilities were 1.58 × 10^-11 for a first parent and 1.08 × 10^-30 for a parent pair. Seven loci showing elevated null allele frequencies were excluded from population structure analyses. Multivariate, phylogenetic and Bayesian analyses revealed no strong genetic subdivision. The developed tools provide practical support for genetic management of alpacas in Poland.