Haplotype and phylogenetic analysis of OLR1(Intron I) gene in Jaffarabadi and Surti buffalo

Abstract

The present study was carried out to reveal haplotype and phylogenetic analysis of OLR1 gene in Jaffarabadi and Surti breeds of buffalo. Twenty nucleotide sequences generated from our previous study (Shabir, 2009) were used to reveal the haplotypes in OLR1 (Intron I) gene in the population of Jaffarabadi and Surti buffalo. Four haplotypes viz. H1 (CTA), H2 (TCT), H3 (CTT) and H4 (TTT) were observed with frequencies of 0.05, 0.1, 0.15 and 0.7 respectively in the population studied. Phylogenetic analysis of these twenty sequences with the same region of Bos taurus distributed the sequences into four clusters based on the homology between them. Cluster I contained two sequences (jb3 and jb8) bearing a common SNP at nucleotide position 843. Cluster III contained s3, s4 and s7 since they possessed a common SNP at nucleotide position 423, however s3 remained as an out group in this cluster since it contained an additional SNP at position 866. The remaining sequences had highest homology and fell in cluster II while as the sequence of Bos taurus remained as an out group on account of the difference in bases at many loci.