Caprine κ-casein (CSN3) polymorphism: new developments of the 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 conformation
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 identified
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 mutations
from the CSN3*F allele. The new variant is
characterized by a G→A transition at nucleotide position
384, resulting in the amino acid exchange Asp90→
Asn90, and a C→T transition at position 550, resulting
in a Val145→Ala145 substitution. Thus, the number
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 geographic
origin with the highest number of alleles found
in goat breeds from the Near East.