Individual goat milk samples, taken from animals of the Indigenous Greek breed and from the international breeds Saanen and Alpine, were studied by RP-HPLC regarding the qualitative and quantitative characteristics of their proteins. Thirty-two samples from the Indigenous Greek breed and 17 from the international breeds were characterised further by RP-HPLC/ESI-MS. The mean total protein content of the milk samples from the Greek breed was higher 38.8 g/l, compared to 31.9 g/l of those from international breeds, due to the great difference between their mean αs1-Cn contents (6.90 and 3.02 g/l, respectively). In the milk samples of the Greek breed, the strong asl-Cn variants B3, B4 and As/Bl predominated, whereas in the milk samples from international breeds the medium variant E and the defectives F and null predominated. Variant A of αs2-Cn followed by variant C and the κ-Cn D (former B) were the most abundant in both groups. αs2-Cn F and the rare κ-Cn variant C/B were observed in the milk samples from the Greek breed. The β-caseins A and C were present in both groups of samples. Finally, the level of phosphorylation of the different genotypes is showed.
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