Physical maps of the ovine PRNP coding sequence, polymorphisms, and assay elements. Panel A features include: thick shaded arrow, coding sequence; black arrow, 3' untranslated region of exon 3; hatched arrows, ovine repetitive elements; white numbered vertical rectangles, octapeptide repeats; vertical lines, positions of SNPs; green single headed arrows, PCR amplification and/or sequencing primers (GenBank AY326330). SNP position numbers are distance to the first base of the PRNP start codon. Letters below SNPs are IUB ambiguity codes (R = a/g, Y = c/t, M = a/c, K = g/t, S = c/g, W = a/t, B = c/g/t, H = a/c/t, D = a/g/t) . Red numbers and letters indicate sites affected by nonsynonymous substitutions at codons 112, 136, 154, 171, and 237. PRNP octapeptide repeats at positions 160 to 285 have either five or six repeats (5rep or 6rep). The asterisks denote SNPs not previously reported. MAF histograms correspond to genotypes from approximately 950 sheep available at http://cgemm.louisville.edu/USDA/index.html. Panel B: Map of ovine PRNP and regions targeted for PCR-amplification. PCR amplicons are depicted as open rectangles. The numbers by green arrows are USMARC primers (see Additional File 2). Panel C: Map of 314 bp PCR-amplified fragment for MALDI-TOF MS testing and expanded histogram of MAF. Features include: large bent blue arrows, PCR-amplification primers with mass tags added; horizontal blue arrows, hME extension primers for MALDI-TOF MS testing.