Evaluation of the application of bovine, ovine and caprine SNP chips to dromedary genotyping

The lack of SNP arrays for less traditional livestock species has led researchers to explore the possibility of applying the use of commercial SNPs already detected in other related livestock species. For example, the medium density bovine and ovine SNP chips have been successfully used to detect polymorphic SNPs in several other species. The dromedary camel belongs to the Camelidae family and represents an important source for production of milk, transportation and meat in several countries. Until now, no SNP chip has been developed for the dromedary and genome information is still incomplete when compared to other livestock species. In this study, 8 to 17 dromedary samples were genotyped using 3 different ruminant species SNP chips: the Bovine 777K SNP BeadChip, the Ovine 600K SNP BeadChip, and the Caprine 50K SNP BeadChip. The quality of hybridization was assessed considering the average value between the 10%GC and the 50%GC (averageGC) scores and the call rate. Only SNPs with averageGC >0.70 and call rate=1.0 were considered. A total of 29,900 Bovine and 14,179 Ovine SNPs were considered successfully genotyped while none of the Caprine SNPs were qualified for further analysis. Among these SNPs, only 27,585 for the bovine and only 88 for the ovine were polymorphic in our dromedary dataset. These SNPs could represent the first step towards the development of a SNP chip useful for this camelid species after appropriate validations.