Genetic structure of the casein gene cluster in the Tunisian native goat breed

The objective was to obtain a description of genetic diversity at the four casein genes in
the Arbi goat, the native goat breed from Tunisia. DNA from 111 Arbi goats (71 females and
40 bucks) was analysed using PCR-based methods. The most frequent allele at the CSN1S1
locus was B, followed by A, F, N, E and 01. The most frequent allele at CSN2 locus was C,
followed by A and 01. The CSN2 E allele was not found. The A, C and F alleles prevailed
at the CSN1S2 locus, the B allele occurred only in one female goat, in heterozygosis. No
subject was found carrying the intermediate CSN1S2 D and the null 0 alleles. The CSN3
A* variant (A + B) prevailed in both sexes on CSN3 C. Five of the estimated haplotypes at
the casein gene cluster CSN1S1–CSN2–CSN1S2–CSN3 showed frequency higher than 0.05:
BAAA(0.155),ACAA(0.150),BACA(0.114),NCAA(0.086) and FCFA (0.060). Three haplotypes
were estimated containing the CSN1S1 E allele, having frequencies lower than 3%. The most
frequent haplotypes contained strong alleles at each casein gene, indicating their possible
positive effect on milk composition and cheesemaking properties. Unexpectedly, two of the
most frequent haplotype combinations contained a null (N) or a weak (F) allele at CSN1S1
locus. Indeed, a casein haplotype combination including the CSN1S1 N allele has not been
evidenced so far in goats. Milk produced from animals carrying these haplotypes could
be suitable for the production of hypoallergenic drinking milk, owing to the low casein
concentration. This information should be taken into account in breeding programs aiming
for genetic improvement of milk characteristics.