Haplotype and phylogenetic analysis of OLR 1 ( Intron I ) gene in Jaffarabadi and Surti buffalo

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.


Introduction
degrades oxLDL, oxidized LDL receptor 1 (OLR1), was initially identified in bovine aortic endothelial Oxidized Low Density lipoprotein Receptor 1 cells (Sawamura et al. (1997).In addition to binding (OLR1) is the major protein that binds, internalizes, oxLDL, OLR1 removes aged and apoptotic cells from and degrades oxidized low-density lipoprotein.The blood circulation (Oka et al., 1998).The bovine OLR1 role of OLR1 in lipid metabolism and the results of gene encodes 270 AA and has 72% identity to the previous whole genome scan studies prompted the human protein (Sawamura et al., 1997).Aoyama et al. investigation of OLR1 as a candidate gene affecting (1999) determined the structure of human OLR1, and milk composition traits (Khatib et. al., 2006).In found 6 exons, of which the first 3 corresponded to the another study conducted in Dutch Holstein-Friesian N-terminal cytoplasmic, transmembrane, and cattle population in OLR 1 gene to estimate genotype connecting neck domains, and the last 3 encoded the effects on milk production traits revealed that lectin domain.The genomic sequence of bovine OLR had a significant effect (P<0.05) on milkg.8232C>A

OLR1, recently released by Baylor College of fat percentage (Schennink et al., 2009). Medicine, contains 5 exons {GenBank accession no. The oxidized form of the low-density NW_215807}. lipoprotein (oxLDL) is involved in endothelial cell
Based on the aforementioned studies indicating injury, dysfunction, and activation, all of which are the role of OLR1 in lipid metabolism and its implicated in the development of atherosclerosis correlation with milk fat percentage, the study of (Mehta and Li, 1998).It has been shown that oxLDL haplotype analysis in this gene in Jaffarabadi and Surti and its lipid constituents have numerous damaging breed of Bubalus bubalis was performed considering effects on secretory activities of the endothelium, the higher milk fat percentages in buffaloes.Also, the including induction of apoptosis (Imanishi et al., phylogenetic analysis at OLR1 gene was done to 2002).The major protein that binds, internalizes, and reveal the genetic distance between the two breeds.

Materials and Methods
Haplotype Analysis: The SNPs detected in OLR1 (Intron I) gene of Jaffarabadi and Surti buffalo in our Phylogenetic analysis: The nucleotide sequences of previous study (Shabir, 2009) were used to carry out OLR1 (Intron I) gene of Jaffarabadi and Surti buffalo the haplotype analysis.The analysis was done by using published in National Centre for Biotechnology the possible number of genotypic combinations of the Information (NCBI) bearing accession numbers Single Nucleotide Polymorphisms (SNPs) that could GQ478023 to GQ478042 (Shabir, 2009) were used to be formed.carry out the phylogenetic analysis of the twenty

Results and Discussion
animals considered in our previous study.The phylogenetic analysis was carried out by MEGA4 Phylogenetic placement of OLR1 gene software.The evolutionary history was inferred using The evolutionary history was inferred using the the Unweighted Pair Group Method with Arithmetic UPGMA method.The optimal tree with the sum of Mean (UPGMA) method.The evolutionary distances branch length of 0.04198671 is shown.The percentage were computed using the Maximum Composite of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) as Likelihood method in the units of the number of base substitutions per site.All positions containing gaps shown next to the branches in Fig. 1.The tree was and missing data were eliminated from the dataset drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the (Complete deletion option).The sample numbers jb1 phylogenetic tree.There were a total of 1147 positions to jb10 correspond to the accession numbers in the final dataset.Phylogenetic analyses were GQ478023 to GQ478032 while as that from s1 to s10 conducted in MEGA4.On phylogenetic analysis of correspond to GQ478033 to GQ478042.

Figure- 1 .
Figure-1.Phylogenetic placement of OLR 1 intron I DNA sequences of Jaffarabadi and Surti breed of Bubalus bubalis and reference sequence of Bos taurus.The databank sequences have been marked by sample numbers .The number around the nodes are confidence levels (%) generated from 500 bootstrap trails.The scale bar is in fixed nucleotide substitutions per sequence position.(Jb = Jafarabadi and S= Surti.