الفهرس 
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Abstract
The objectives of this study were to investigate the genetic structure of the casein genes in some Egyptian and Italian breeds, evaluate the genetic variability at the casein alpha S1 in these breeds and studying the relationships among and within the Egyptian and Italian goat breeds.
Two Egyptian goat breeds, Zaraibi (n=21) and Barki (n=24) and 2 Italian breeds, Nicastrese (n=24) and Aspromonte (n=8), were used in the present study.
PCR and PCR-RFLP (Restriction Fragment Length Polymorphism) methods were used to identify CSN1S1 alleles A, B, E, F, N and 01. Allele Specific Polymerase Chain Reaction (AS-PCR) method was used to distinguish between alleles CSN1S1-A and CSN1S1-01. ASA-PCR was carried out in order to identify alleles B and E. Concentration and composition of alpha S1 casein protein in milk are controlled by polymorphism in CSN1S1 gene. The genotypes AB and BB were the most frequent (0.163) in the Egyptian populations while the genotype AA showed the highest frequency (0.258) in the Italian populations. The genotype AA showed a high frequency in Barki (0.182). AB, BB and NB genotypes were the highest in Zaraibi breed (0.190) while other genotypes frequency represented less than 43%. CSN1S1 showed high frequency of strong alleles, A and B, in the Egyptian breeds. In Barki breed, CSN1S1 strong alleles were represented by about 61%. CSN1S1-01 allele has been detected only in Barki breed with low frequency (0.045). Strong alleles A and B showed high frequencies, about 69%, in Zaraibi breed. Barki showed the highest expected heterozygosity (0.742) followed by Zaraibi (0.689). Studying genetic differentiation and Wright’s F statistics, Positive FIS was observed in all studied populations except Zaraibi. Large genetic diversity was detected in the Egyptian breeds in the present study. Italian breeds showed low genetic diversity in the null alleles. This low variability may be due to the selection applied and/or the isolation of these breeds in the mountain area in Calabria region, Italy. All studied populations were in HW equilibrium. Genetic differentiation (FST) showed similarity between Egyptian populations. Standard genetic distance ranged from 0.041 between Barki and Zaraibi to 0.405 between Zaraibi and Aspromonte. Low genetic distance observed within the Egyptian populations and within the Italian breeds. Phylogenetic tree separated both Egyptian and Italian breeds into two clusters. Geographic separation and the non exchange of genetic material among Mediterranean breeds have lead to this apparent genetic dissimilarity between Egyptian and Italian breeds.
The A, B, C, E and F CSN1S2 alleles are associated with normal αs2 casein protein synthesis level (about 2.5 g/L), whereas alleles D and 0 are associated with low and null synthesis levels, respectively. For identifying different alleles in the CSN1S2 locus, PCR and NcoI endonuclease RFLP was used to analyze Egyptian and Italian breeds. The gel electrophoresis of Barki, Zaraibi and Aspromonte breeds showed two fragments (168bp + 133bp) which indicate that these breeds carry CSN1S2 A, B, C, F or E which associated with normal casein S2 protein in milk. The intermediate allele CSN1S2-D was absent in all breeds. The null allele CSN1S2-0 was not found in Egyptian breeds. CSN-0 allele was observed with low frequency (0.04) in Nicastrese breed. The genetic profile of the Egyptian breeds in CSN1S2 locus indicates the good level of casein alpha S2 protein in milk which has an important role in cheese production.
The genetic polymorphism of the CSN2 is controlled by 8 alleles, six of them, A, A1, B, C, D, and E, are associates with the normal beta casein protein content in milk while two null alleles, CSN2-0 and CSN2-0’, are associated with the absence of the beta casein protein in milk. PCR was held to identify CSN2-A allele and CSN2-0. There was no polymorphism found at CSN2 locus in Barki and Zaraibi breed. The Egyptian breeds carried only the A allele. Allele 01 was in low frequency in Nicastrese breed (0.04) and in a frequency of 0.19 in Aspromonte breed. The use of the Egyptian goat milk with the normal B-CSN content in cheese may have an additional value for producing high quality cheese since the presence/absence of CSN2 null allele is associated with the milk properties and cheese quality.
The coding sequence of k-casein for the exon 4 was amplified by PCR primers I3F and Kb2. Sequencing analysis was carried out in order to detect new polymorphisms in the Egyptian breeds. Genotype CSN3B/B appeared in all the tested animals. No new polymorphism was found in the Egyptian breeds. Egyptian breeds carrying the favorable CSN3-B allele could be considered as an evidence for the normal K casein protein contents of the Egyptian goat milk. Results indicate that Egyptian breeds have a considerable genetic structure with high variability and carrying the favorable casein alleles in high frequency. They may be considered as valuable genetics resources to be used in milk production and cheese industry. Genotyping of the casein genes will help in selecting females and males in early stages for milk production. Gene Assisted Selection (GAS) makes direct selection of males in sex-limited traits, as milk protein, possible. Using this strategy will reduce time and efforts in establishing breeding program for Egyptian breeds.