The aims of this study were to analyze sequence variability within genes related to important economic traits in dairy and non-dairy sheep breeds, and to evaluate the genetic variability as an insight into their development. In total, 31 single nucleotide polymorphisms (SNPs), one indel, and one microsatellite, all located in ovine milk protein genes (CSN1S1, CSN1S2, CSN2, CSN3, LGB), and 13 SNPs located in genes associated with production and reproduction traits of economic importance (DGAT1, DGAT2, GHR, FASN, GHRHR, CTSB, MCR1, KRT1, IL2, IGF1, HR, GDF8, GDF9) were genotyped. The analysis included 752 samples derived from 23 different European, Middle-Eastern (Turkey and Israel) and African (Nigeria and Cameroon) sheep breeds, and the European Mouflon.

We could not observe the often described decline of heterozygosity with increasing distance to the domestication centre maybe because of high gene flow and gene introgression between breeds following domestication. Tendencies of clustering according to the local origin of the animals were visible, whereas a clear breed grouping was not identified. No significant difference was found by principal component analysis of casein haplotypes between dairy and non-dairy breeds. However, using Canonical Discriminant Analysis most of the non-dairy individuals were correctly assigned to the non-dairy group, with an increasing precision when considering both casein haplotypes and the remaining SNP. The distribution of variation in the production-related SNP analyzed reflects both the long history of migrations, adaption, isolation, and the most recent effect of gene flow or isolation due to selection in the different breeds.