Comparison of casein haplotypes between two geographically distant European dairy goat breeds

The aim of this paper was to characterize the diversity among haplotypes based on 22 single nucleotide polymorphisms (SNPs) and one deletion within four casein genes in two geographically distant goat populations, the Sicilian Girgentana breed and the Norwegian goat breed. Forty Girgentana goats were genotyped for the aforementioned polymorphisms and the resulting data set was compared with 436 goats from the Norwegian population previously genotyped for these markers. Several casein gene polymorphisms were not in Hardy-Weinberg equilibrium either in Girgentana, or in the Norwegian breed. The SNP haplotype frequencies for the four casein genes were calculated and despite the large geographical distance and phenotypic divergence between these breeds, a proportion of casein loci haplotypes were found to be identical between both Norwegian and Girgentana goats. However, for the CSN2 gene there were no common haplotypes between the two populations. The level of linkage disequilibrium between the casein genes was less in the Girgentana population than in the Norwegian population.