Examination of D-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations

Abstract

Hybridisation between alpacas (Vicugna pacos) and llamas (Lama glama) is a well-known phenomenon among alpaca breeders worldwide. Hybridisation causes poor fibre quality, which leads to economic losses. In the present study, we aimed to evaluate the d-loop region of mitochondrial DNA and the DBY gene located on chromosome Y to identify alpaca × llama hybrids. Moreover, based on these tools, the genetic diversity of alpacas in Poland was presented. We analysed the d-loop region in 235 individuals and investigated 90 pure males for the DBY gene. We generated 34 haplotypes with 446 segregation sites for the d-loop region and two haplotypes with four segregation sites for the DBY gene. Phylogenetic analysis based on the Bayesian clustering approach and a principal coordinate test showed a high level of mitochondrial DNA introgression between alpacas and llamas with a high gene flow value based on the sequence and on the haplotype data information. We found evidence of maternal line hybridisation in the d-loop region between alpacas and llamas, while this evidence was not found within the DBY gene. Moreover, the d-loop region investigation showed high levels of genetic diversity in the alpacas maintained in Poland.