Caprine κ-casein (CSN3) polymorphism: New developments in molecular knowledge

A high degree of polymorphism was recently found at the κ-casein (CSN3) locus in the domesticated goat (Capra hircus). In the present study, 2 new patterns previously identified by PCR-single-strand conforma- tion polymorphism analysis (SSCP) were characterized. The allele provisionally named “X” (GenBank Accession no. AY350425) differs from CSN3*C (AF485341) by a (silent) A→G substitution at position 509 of the goat CSN3 reference sequence (X60763). As this newly iden- tified sequence changes the amino acid sequence, and the already known CSN3*C allele (AF485341) has an additional silent mutation, we proposed a change in nomenclature to reflect these changes, indicating the silent mutation with the prime symbol (i.e., ′). The CSN3*M allele (provisionally named “Y”) results in a new protein variant, differing by 2 nonsynonymous mu- tations from the CSN3*F allele. The new variant is characterized by a G→A transition at nucleotide posi- tion 384, resulting in the amino acid exchange As- p90→Asn90, and a C→T transition at position 550, re- sulting in a Val145→Ala145 substitution. Thus, the num- ber of alleles identified in the domesticated goat has increased to 16, of which 13 are protein variants and 3 are silent mutations, involving a total of 15 polymorphic sites in CSN3 exon 4. Data on the distribution of the main alleles in 7 goat breeds of Europe, West Africa, and the Near East show differences in the occurrence and frequency of the alleles between breeds and geo- graphic origin with the highest number of alleles found in goat breeds from the Near East.