First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants.

This study investigated polymorphisms in the milk protein genes , , , , , and , and casein haplotypes in Beninese indigenous cattle. Considering 67 animals, DNA sequencing of the genes' exons, flanking regions and parts of the 5'-upstream regions identified 1058 genetic variants including 731 previously unknown. In addition, four novel milk protein variants were detected, including (p.Ala66Val), (p.Arg58Trp), (p.Ala134Val) and (p.Thr92Asnfs*13). is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas and are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding , a frameshift insertion of one adenine residue at BTA11:103257980 (exon 3) induces a premature translation termination resulting in a 46% reduction of the reference protein sequence. The casein polymorphisms formed five main haplotypes including B-A1-A-B, B-A1-A-A and C-A2-A-B which are predominant in the investigated cattle breeds. Moreover, in silico analyses of polymorphisms within the 5'- and 3'- untranslated regions of all six milk proteins revealed effects on microRNA and transcription factor binding sites. This study suggests a large genetic variation of milk protein genes in Beninese cattle, which should be investigated in further studies for their effects on milk production, including quality and yield traits.