New genetic polymorphism at the αs1-casein gene region in Ethiopian indigenous goat breeds

Part of the 5′ flanking region, 12 introns and 10 exons of the αs1-casein gene were genotyped in 326 goats from 10 indigenous Ethiopian goat breeds. This study was conducted with an attempt to reveal genetic variation at regions of the αs1-casein gene. A total of 37 previously unreported SNPs: 3 in exons, 3 in the 5′ UTR, and 31 in the introns were detected. At nucleotide position of 6072 and 12465 that corresponded to amino acid positions 15 and 100 of mature protein, synonymous transitions GTC → GTT (Val15) and AGA → AGG (Arg1 0 0) were detected. The third mutation gave rise to a non-synonymous transversion at nucleotide position 10657 resulting in shift of amino acid Gln77 → Pro77 of the mature protein. The two amino acids, Glutamine and Proline, have different properties which can possibly affect the property of the mature protein. Significantly high linkage disequilibrium (P < 0.01) between the alleles was observed in all breeds. The findings of this study are of considerable scientific and economic importance for the on-going goat breed improvement programs in Ethiopia. Future work should focus on evaluating the effect of the SNPs in the 5′ UTR and assessing the effect of the mutation in the exon region on milk quality and technological parameters. This work should be extended to the remaining regions and the other casein genes.