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.