Understanding functional implication of β-casein gene variants in four cattle breeds characterized using AmpliSeq approach

Here, we designed a custom panel targeting whole β-casein gene SNPs of zebu and taurine cattle breeds to identify variants and applicability in dairy cattle genotyping. We sequenced two libraries consisting of different pools of primer sets from 95 individuals on the Illumina MiSeq. Consequently, over 92% target regions were amplified and 71 SNPs were available after quality filtering. Only three intronic variants were novel while majority of the identified variants were catalogued in dbSNP as known variants. Identified missense SNPs lead to variant A1/A2, B, F and A3, located in exon 7 only. For confirmation, A1/A2 locus was genotyped using PCR–RFLP. Variant B was observed in all animals, either in homozygous or in heterozygous form. Variants A1, F and A3 predicted to have a deleterious effect on protein function by decreasing the structural stability. Additionally, SIFT score revealed that the A1 variant might affect the protein function.