Genome research has progressed rapidly in recent years and DNA-based selection tools are now available in a number of domesticated species. To date, advanced genomics technologies have not been developed in alpacas (Vicugna pacos). Therefore, breeders select for traits of economic importance (fleece phenotypes) using traditional techniques such as line breeding. Alpacas have experienced a history of population bottlenecks including the mass destruction of alpacas and llamas during the 16th Century, therefore traditional breeding may exacerbate an already depleted gene pool. Alpaca veterinarians report a prevalence of congenital defects much higher than any other livestock species. This study investigated levels of genetic diversity at genome-wide markers in Australian alpacas. Samples have been collected from unrelated individuals with normal and defective phenotypes including choanal atresia, polydactyly, cyclopia, syndactyly, vulval atresia and anal atresia. Multi-locus heterozygosity and inbreeding coefficients were estimated using microsatellite data from 53 or 22 loci. In addition, pedigrees were examined in order to detect pedigree inbreeding. Inbreeding coefficients estimated from genomic data reveal that individuals with congenital defects do not have significantly higher molecular inbreeding levels than healthy individuals. These results suggest that high levels of inbreeding cannot explain the high prevalence of congenital abnormalities in alpacas. This study is the first to report on the genetic variability of Australian alpacas and represents an important first step in the use of genomics to inform alpaca breeding practices.
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