Molecular differentiation of Peroxysome proliferator activated receptor coactivator-1 among different breeds of Bubalus bubalis

Peroxysome proliferator activated receptor coactivator-1 gene (PPARGC1A) is a positional and functional candidate gene for milk fat yield. It has key role in energy, fat and glucose metabolism. Single nucleotide polymorphisms (SNPs) in Exon-8 of PPARGC1A are reported to be associated with milk fat yield in dairy cattle. In the present investigation PPARGC1A was partially amplified (around 767bp) by designing gene specific primer and confirm by sequencing the amplicon and its comparison with the PPARGC1A gene of bovine. Comparative study of PPARGC1A among different breeds of buffaloes reveals different level of mutations with respect to its gene sequence 0.013-1.69% and protein sequence 0.42% to 2.99%, Similarly the protein structures modeled from their sequences were compared by structural superposition that shows variations (RMSD) from 0.736 to 1.507. Furthermore, the sequences were used to generate a dendrogram. It reveals that Murrah and reference are very close to each other, similarly Toda, Bhadawari and Surti are closely related, whereas Pandharpuri is separated from both the cluster. Especially the variations are more at the binding site of this protein that may be the cause that different breeds have different percentage of milk fat. Further study is underway to detect polymorphism and associate them with milk fat related traits in buffalo.