Genetic diversity and population structure in divergent German cattle selection lines on the basis of milk protein polymorphisms

The aim of this study was to analyze the genetic structure of the casein cluster in eight selection lines of the Holstein Friesian (HF), German Simmental (GS) and German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind”, DSN) breeds. A total of 2962 milk samples were typed at [Formula: see text]-casein ([Formula: see text]-CN), [Formula: see text]-casein ([Formula: see text]-CN), [Formula: see text]-casein ([Formula: see text]-CN) and [Formula: see text]-casein ([Formula: see text]-CN) loci using isoelectric focusing. The number of alleles per locus ranged from one ([Formula: see text]-CN) to five ([Formula: see text]-CN), and the average expected heterozygosity and polymorphic information content of all loci were 0.33 and 0.27, respectively. The unrooted dendrogram revealed that the selection lines of the endangered DSN breed were clearly separated from the HF and GS breeds due to their predominance of the [Formula: see text]-CN A1 allele and the comprehensive haplotype BA1A (in the abbreviation of [Formula: see text]- [Formula: see text]- [Formula: see text]-CN). Temporal changes in allele distributions indicated decreasing genetic diversity at the casein loci, explaining the moderate level of genetic differentiation among selection lines (7.1 %). The variability of the casein should be exploited in future using breeding programs to select genetic lines for specific protein production in bovine milk but also to preserve biodiversity.