Identification of two new alleles at k-casein (CSN3) gene in Girgetana goat breed

In the milk of ruminants, more than 95% of proteins are synthesized by six structural genes, four caseins and two whey proteins. The κ-casein fraction plays an important role in the formation, stabilization and aggregation on casein micelles and thus affects technological and nutritional properties of milk. Goat κ-casein (CSN3) gene comprises five exons with the mRNA coding region for mature protein spanning from exon 3 to exon 4. The κ-casein locus has been widely investigated and several genetic variants have been found in different goat breeds. At protein level, AIEF and BIEF groups corresponding to isoelectric point 5.53 and 5.78, respectively, have been identified. In this study, exon 4 of CSN3 gene was sequenced and analyzed in 205 samples of Girgentana goat breed. Analyses of the obtained sequences showed the presence of A, B, D, and G known alleles and two new genetic variants, named D' and N. The new D' allele differing from D in one transition G284→A284 that did not cause amino acid change. The new N allele differing from A for five SNPs T245/C245, G284/A284, G309/A309, G471/A471, and T591/C591. Comparing the amino acid sequences of N and A alleles, the first two SNPs caused no amino acid change, whereas the other SNPs produced changes Val65/Ile65, Val119/Ile119, and Ser159/Pro159, respectively. The most frequent allele was A (0.480) followed by B (0.363), D (0.112), and N (0.034). The D' and G alleles were identified only in two animals and in heterozygous conditions with a very low frequency (0.005). The most common genotype was AB (39.5%) followed by AA (19.5%), AD (12.7%), and BB (11.7%). Homozygous D'D', GG, and NN individuals were not found. Among the CSN3 alleles found in our study, only the D and D' alleles are included in BIEF group, whereas A, B, G and N alleles belong to AIEF group, which represents the less favorable variants’ group in terms of milk composition and technological properties. Several authors reported that some genotypes at CSN3 locus were associated with higher level of total casein and protein content than others. Therefore, further analysis will be performed in order to establish associations among genotypes and quantitative and qualitative milk traits.