Characterization of single nucleotide polymorphisms [SNPs] in the 5'-flanking region of bovine lactoferrin gene in the local and Holstein cattle of Iran

ABSTRACT

Lactoferrin [Lf], an iron binding glycoprotein, has a variety of physiological roles and its foremost is antimicrobial properties. Therefore, the lactoferrin gene can be considered as a potential candidate gene for resistance to mastitis. This study was carried out to determine the haplotype frequency of the 5'-flanking region of bovine lactoferrin gene in local and Holstein cattle breeds of Iran using PCR-SSCPand DNA sequencing. Genomic DNA was isolated from 100 blood samples of two cattle breeds [50 Local, 50 Holstein]. Two new primer pairs were designed from Lf sequence to amplify a part of 5'-flanking region of the gene. The amplified fragment was screened by single strand conformation polymorphism [SSCP] and DNA sequencing. The multiple alignments were carried out for the nucleotide sequences of different SSCPpatterns. In silico analysis of identified single nucleotide polymorphisms [SNPs] within the 5'-flanking region of bovine Lf gene was screened, to identify any association on transcription factor binding affinity. Analysis of the whole samples revealed three SSCP patterns [A, B and C] for amplified fragment that C haplotype was the only variant identified in local breed samples. The bioinformatics analysis revealed that the Tto G trans version at position -602 created an AML-1 transcription binding site in combined genotype A. In -586 position, Tto C transition abolished binding site of AML-1 transcription factor. Therefore, to apply Lf gene for marker-assisted selection, additional studies are required to evaluate the functional role of these identified polymorphic sites on gene expression and somatic cell counts in cattle