Document Type : Research Paper
Authors
1
Department of Animal Science, College of Agriculture, University of Tehran, Karaj, Iran
2
Department of Animal Science, College of Agriculture, Arak University, Arak, Iran
3
Department of Animal Science, College of Agriculture, University of Tehran, Jolfa, Iran
Abstract
Bovine leukemia virus infection is more prevalent in dairy herds and so far there is no known cure or vaccine for this disease. This research aimed to conduct a genome-wide scanning (GWAS) study to identify genomic regions and candidate genes associated with BLV infection. This study was conducted using Iranian Holstein cows that were naturally infected with BLV. For this purpose, blood samples were collected from 150 Holstein cows in an industrial cattle farm in Isfahan, and DNA and serum were extracted from them. Then the prepared DNA samples were genotyped using k30 chips (SNPchip30k). Quality control of genotyped markers based on rare allele frequency indices (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05) and Hardy-Weinberg balance (PH-W <1×10-6) was performed by PLINK software. After the quality control analysis, 140 cows (77 patients and 68 controls) and 22868 markers remained for further analysis. After performing the genome scan analysis in the PLINK program, eight markers above the significance threshold were finally identified. Then, by bioinformatic analysis of significant genomic regions using online ensemble databases and genecards, genes associated with significant markers were identified, the most important of which include GRK4, TP53BP1, SCAPER, GLRB, PDGFC, TNIP2, PSTPIP1, CEP350, MR1, TOM1L2, SREBF1, COPS and TNFRS13B. Gene Ontology (GO) analysis showed that these genes are mostly involved in regulating enzyme activity, DNA stability, lipid activity, antiviral response, innate immune response, and disease resistance.
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