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A new alternative genotyping method based on PCR-SSCP was developed for direct differentiation of the CSN1S1 alleles B and C in the coding region. In addition a PCR-RFLP test based on a MaeIII restriction site in the promoter region of CSN1S1, reported in the literature as an alternative test for the differentiation of CSN1S1*B and C was used and the alleles named b and c. Genotyping of 649 animals belonging to 17 European and Turkish cattle breeds showed differences in occurrence and frequency of the alleles. CSN1S1*B occurred in all breeds with frequencies varying from 0.50 in Anatolian Blackup to 1.0 in e.g. Ayrshire. CSN1S1*b on the other hand varied from 0.63 in Jersey, 0.97 in Ayrshire to 1.0 in e.g. Angler. Comparison of the results from both typing methods and positions in the gene showed that both mutations do not always occur together. From the resulting four intragenic haplotypes (B-b, B-c, C-c and C-b) B-b is predominant in all breeds with frequencies varying from 0.3450 in Anatolian Black to 1.0 in Angler and Scottish Highland. The number of haplotypes varied from only one in Angler and Scottish Highland, two in Ayrshire, three in Asturian Valley and Turkish Grey Steppe to all four in the other 12 breeds. Correlation between allele frequencies and the geographic origin of the breeds was significant for the MaeIII promoter polymorphism

Intragenic haplotypes at the bovine &lt;i&gt;CSN1S1&lt;/i&gt; locus

Intragenic haplotypes at the bovine <i>CSN1S1</i> locus