Allele frequencies for SNPs in the αS1-casein gene (CSN1S1) 5′ flanking region in European cattle and association with economic traits in German Holstein

Allele frequencies of a polymorphism in the αS1-casein 5′ flanking region (CSN1S1-5′) were determined in 14 Central and Eastern European cattle breeds by single strand conformation polymorphism analysis. Allele frequencies ranged from 0.00 to 0.35 (allele 1), 0.08 to 0.91 (allele 2), 0.04 to 0.41 (allele 3) and from 0.00 to 0.16 (allele 4). Allele 5 was not found. Presence of allele 2 in all breeds highlights its probable wild type status. A loss of alleles and genotypes occurred in some breeds, but differentiation within the breed groups milk, beef and dual purpose was higher than between these groups. An analysis of the variance in a German Holstein granddaughter design with family and CSN1S1-5′ genotype as fixed effects revealed significant effects (P < 0.05 each) of the CSN1S1-5′ genotype on breeding values for dairy character, fore udder attachment, length of productive life and highly significant effects on somatic cell score (P < 0.001). Genotype LS-means assigned favourable values for udder health and longevity to genotype 24. Past selection for milk yield or beef production does not seem to have favoured indirectly specific promoter alleles. No negative effects of genotype 24 were evident in Holstein, but selection for 23 requires careful inspection of unfavourable side effects.