Characterization and multiplex genotyping of alpaca tetranucleotide microsatellite markers

Hybridisation-capture was used to create 12 unique alpaca DNA libraries each enriched for a different tetranucleotide microsatellite motif. Two hundred and forty-nine microsatellites were found, of which 26 were polymorphic (motifs GGAT, GTTT and GCAC). Nine markers were fully characterised on 45 samples. Allele numbers ranged from 6 (locus P135) to 12 (loci P149 and PCTD17). There was no evidence of linkage disequilibrium at any locus (p = 0.064–1). Deviation from Hardy–Weinberg equilibrium was observed in three loci after Bonferroni correction (PCTD17, P135 and P193). Null alleles were detected at loci P147, P193 and P194. Polymorphic information content ranged from 0.48 to 0.82. When combined, the markers had an exclusion probability of 97.7%. Two polymerase chain reaction multiplex sets comprising six and three markers each were optimized. These multiplex sets will be useful for parentage determination, and individually the markers will add to the pool of markers available for mapping of desirous or deleterious traits in alpacas.