Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 24, 2006
Publication Date: November 8, 2006
Citation: Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2006. Prion gene haplotypes of U.S. cattle. BioMed Central (BMC) Genetics. 7:51. Interpretive Summary: Transmissible spongiform encephalopathies (TSEs) are fatal neurological disorders that are characterized by abnormal deposits of the prion protein. TSEs have been identified in cats, cattle, deer, elk, humans, mink, moose, and sheep. The cattle TSE, bovine spongiform encephalopathy (BSE) is also known as mad cow disease. BSE is the probable cause of the human TSE variant Creutzfeldt-Jakob disease, transmitted from cattle to people via the food chain. Sequence variation in the prion gene correlates with TSE progression in humans, sheep, and mice. Additionally, there is evidence that bovine PRNP variation correlates with BSE progression. In this study, 25.2 kb of PRNP was sequenced from the promoter region through the three prime untranslated region in 192 U.S. cattle (16 beef, five dairy breeds). Three hundred and eighty eight polymorphisms were observed, of which 287 have not been previously reported. A subset of polymorphisms that efficiently tag genetic variation in U.S. cattle was identified. The results of this study provide a reference framework for accurate and comprehensive evaluation of prion gene variation and its relationship to BSE.
Technical Abstract: Background: Bovine spongiform encephalopathy (BSE) is a fatal neurological disorder characterized by abnormal deposits of a protease-resistant isoform of the prion protein. Characterizing linkage disequilibrium (LD) and haplotype networks within the bovine prion gene (PRNP) is important for 1) testing rare or common PRNP variation for an association with BSE and 2) interpreting any association of PRNP alleles with BSE susceptibility. The objective of this study was to identify polymorphisms and haplotypes within PRNP from the promoter region through the 3'UTR in a diverse sample of U.S. cattle genomes. Results: A 25.2-kb genomic region containing PRNP was sequenced from 192 diverse U.S. beef and dairy cattle. Sequence analyses identified 388 total polymorphisms, of which 287 have not previously been reported. The polymorphism alleles define PRNP by regions of high and low LD. High LD is present between alleles in the promoter region through exon 2 (6.7 kb). PRNP alleles within the majority of intron 2, the entire coding sequence and the untranslated region of exon 3 are in low LD (18.0 kb). Two haplotype networks, one representing the region of high LD and the other the region of low LD yielded nineteen different combinations that represent haplotypes spanning PRNP. The haplotype combinations are tagged by 19 polymorphisms (htSNPS) which characterize variation within and across PRNP. Conclusion: The number of polymorphisms in the prion gene region of U.S. cattle is nearly four times greater than previously described. These polymorphisms define PRNP haplotypes that may influence BSE susceptibility in cattle.