The aim of this study was to develop a preliminary physical map of single nucleotide polymorphisms (SNPs) in alpaca using an alpaca/hamster radiation hybrid panel and a bovine high- density SNP genotyping microarray (BovineHD BeadChip-Illumina). The methodology included genotyping 92 alpaca/hamster hybrid cell clones, and four control samples (male alpaca, female alpaca, hamster and 1:10 DNAmixture) with the microarray. After genotyping the alpaca and hamster DNA control samples, only bovine SNPs with a call frequency of 1 were retained. The SNPs identified in the alpaca DNA samples were then filtered to remove those also found in the hamster. From the remaining alpaca SNPs, to decrease the probability of false positives, only those with a call frequency from 0.2 to 0.8 in the 92 hybrid clone samples were retained for the final analysis. The remaining alpaca specific SNPs were tabulated ...

This research was supported by FONDECYT, Chile Grant 1140785, Postdoctoral Grant 3050046 and CONICYT Chile (Beca de Apoyo a Tesis Doctoral), Morris Animal Foundation (D05LA-002), Darwin Initiative for the Survival of Species (United Kingdom) 1312 grant 162/06/126, The British Embassy (Lima), NERC 1313 (United Kingdom) grant GST/02/828, and Newton Fund Researcher Links Travel grant (ID: RLTG9-LATAM-359537872) funded by the UK Department for Business, Energy and Industrial Strategy and CONCYTEC (Peru) and delivered by the British Council.