Analysis of genetic variations across regulatory and coding regions of kappa-casein gene of Indian native cattle (Bos indicus) and buffalo (Bubalus bubalis)

The promoter region of kappa-casein (κ-CN) gene in Indian native cattle and buffalo breeds was sequenced and analyzed for nucleotide variations. Sequence comparison across breeds of Indian cattle revealed a total of 7 variations in the promoter region, of which − 515 G/T, − 427 C/T, − 385 C/T, − 283 A/G and − 251 C/T were located within consensus binding sites for octamer-binding protein (OCT1)/pregnancy specific mammary nuclear factor (PMF), activator protein-2 (AP2), hepatocyte nuclear factor (HNF-1) and GAL4 transcription factors (TFs), respectively. These variations might be involved in gain or loss of potential transcription factor binding sites (TFBSs). Unlike the other 4 variants, the − 283 (A/G) variant located within HNF-1 TFBS was specific to Indian cattle as this change has not been observed in the Bos taurus sequence. Other TFBSs viz., MGF, TBP, NF-1, milk box and C/EBP were conserved across species. For the Indian native buffalo breeds, only 3 changes were identified in the promoter region; − 305 (A/C), − 160 (T/C) and − 141 (A/G) and most of the TFBSs were found to be conserved. However, deletion of two adjacent nucleotides located in and around binding site for C/EBP TF was identified in buffalo when compared with promoter sequence of bovine κ-CN. For κ-CN of Indian native cattle, a strong linkage disequilibrium (LD) was observed for variations 515 G/T, − 427 C/T and − 385 C/T in the promoter region; and for variations at codons 136 and 148 of exon-IV. Further, among intragenic haplotypes, variation − 427 C/T was found to be in LD with variations at codons 136 and 148. The information generated in the present work provides comprehensive characterization of κ-CN gene promoter and coding regions in Indian cattle and buffaloes and reported variations could become important candidates for carrying out further research in dairy traits.