Transmissible spongiform encephalopathies (TSEs) are a class of neurodegenerative diseases that affect various mammals, including cattle, sheep, mink, cervids, and humans. They are caused by abnormally folded prion proteins that induce the conversion of the normal and non-infectious cellular form of the host prion protein (PrPC) into the abnormal and infectious form (PrPSc) . Susceptibility or resistance to a TSE can be influenced by several factors of the host prion protein, such as specific amino acid polymorphisms, the number of octapeptide repeats present, and prion protein expression levels. These 3 factors are all relevant to prion biology in cattle.
Bovine spongiform encephalopathy (BSE) is a TSE of cattle. Based upon Western blot and in vivo analysis, BSE can be differentiated into two strains, classical and atypical BSE [2–4]. Although amino acid differences in the prion protein are a major component in susceptibility and resistance to TSE disease in humans  and sheep , they are not associated with classical BSE cases in cattle. However, the prion protein gene (PRNP) for the 2006 US atypical BSE case encoded an amino acid change in one allele at bovine codon 211 (Glutamic Acid → Lysine; E211K) . This change is analogous to the human E200K amino acid replacement, which is associated with the leading cause of heritable TSE disease in humans . To date, the E211K change has been reported in only two bovine samples, the atypical BSE-positive cow  and its only known living offspring .
The octapeptide repeat region is a series of amino acid repeats near the N-terminal portion of PrPC, has been implicated in binding divalent cations, and may affect the structure and function of the prion protein . Humans, sheep, and cervids (deer) normally possess 5 octapeptide repeats, while cattle typically have 5 or 6 repeats [10, 11]. The presence of extra repeats encoded within the octapeptide region is correlated with an increase in TSE susceptibility, as has been observed in humans that possess more than 5 octapeptide repeats [12, 13]. Additionally, transgenic mice expressing bovine PrPC containing 7 or 10 repeats are also more susceptible when challenged with BSE [14, 15]. Of the breeds tested to date, only Brown Swiss cattle are known to encode 7 octapeptide repeats [16, 17], and they have been reported to be more susceptible to BSE than other cattle breeds [18, 19]. These data suggest that bovine PrPC containing 7 or more octapeptide repeats may enhance susceptibility to BSE.
In addition to qualitative changes in the mammalian prion protein itself, the level of mammalian PrPC expression is also known to influence susceptibility or resistance to a TSE disease. Over-expression of PrPC in transgenic mice challenged with a TSE resulted in shorter incubation periods as compared to wild type mice [20, 21]. Conversely, transgenic mice possessing one functional PRNP allele had decreased expression levels of PrPC, which led to a longer incubation time after a TSE inoculation . Mice lacking functional PRNP alleles (Prnp
0/0) were resistant to TSE challenge . In cattle, two non-coding polymorphisms have been associated with PrPC expression levels [24, 25]. The first is a 23-bp deletion within the promoter region that removes a binding site for the RP58 repressor protein, and the second is a 12-bp deletion within intron 1 that removes a SP1 transcription factor binding site . Cattle possessing these deletions, and therefore lacking binding sites for their respective regulatory elements, have been reported to be more susceptible to classical BSE [24, 26]. These polymorphisms do not influence resistance to atypical BSE [27, 28].
To date, most analyses of cattle populations for these specific BSE susceptibility factors have focused on breeds derived from Bos taurus. However, few relevant studies currently exist for Bos indicus or B. indicus × B. taurus composite cattle. Since B. indicus purebred and composite cattle are dispersed throughout the world, we elected to determine the frequencies of known genetic factors associated with BSE susceptibility and resistance in a diverse sample intended to represent the global population. In this report, we provide a detailed comparative analysis of the 23-bp promoter region, 12-bp intron region, and relevant PRNP polymorphisms for B. indicus, B. taurus, and B. indicus × B. taurus composite cattle. Differences in the frequencies of these established risk factors may also elucidate differences in overall resistance and/or susceptibility to classical BSE between the cattle groups investigated.