| Summary: | This study investigated polymorphisms in the milk protein genes <i>CSN1S1</i>, <i>CSN2</i>, <i>CSN1S2</i>, <i>CSN3</i>, <i>LALBA</i>, and <i>LGB</i>, 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 <i>CSN3<sup>K</sup></i> (p.Ala66Val), <i>LALBA<sup>F</sup></i> (p.Arg58Trp), <i>LGB<sup>B1</sup></i> (p.Ala134Val) and <i>LGB<sup>K</sup></i> (p.Thr92Asnfs*13). <i>CSN3<sup>K</sup></i> is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas <i>LALBA<sup>F</sup></i> and <i>LGB<sup>B1</sup></i> are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding <i>LGB<sup>K</sup></i>, 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 <i>CSN1S1-CSN2-CSN1S2-CSN3</i> 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.
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