2006 Annual Report
Identification of polymorphisms in the bovine prion gene. A 25.2-kb genomic region encompassing the bovine prion gene (PRNP) was sequenced in panels representing the breadth of genetic diversity in U.S. beef and dairy cattle (n=192 individuals). Each amplicon spanning this region had greater than 95% coverage of cattle with high quality sequence (Phred score > 20). Sequence analyses identified 388 total polymorphisms, 350 single nucleotide polymorphisms (SNP) and 38 insertion/deletions, of which 287 have not previously been reported. The polymorphisms define PRNP by regions of high and low linkage disequilibrium (LD), an indicator of highly linked polymorphisms. 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.
Sequencing of the rest of the prion gene complex, including the PRNP paralogs PRND (doppel) and PRNT is underway. The region between PRNP and PRND, a distance of 26 kb, was found to consist largely of large repetitive elements rendering it relatively intractable to amplification sequencing. An approximately 8 kb region containing PRND has been largely sequenced and annotation of polymorphisms is underway. Sequencing of the approximately 7 kb region surrounding PRNT is in progress.
Impact: Work to date increased the number of polymorphisms identified in the bovine PRNP nearly 4-fold. Haplotype combinations from each of the LD regions effectively capture PRNP diversity in U.S. beef and dairy cattle and define a PRNP reference haplotype framework which can be used to test specific haplotype combinations for association with BSE susceptibility.