BAVARIAN RESEARCH ASSOCIATION PRIONS
TUM 9 BSE Genomics B
We aimed to investigate several candidate genes for an association with BSE susceptibility. All together, ten genes were analyzed, which were either located in putative candidate regions as revealed by whole-genome marker scans and/or were implied as functional candidate genes because their gene product is supposed to be involved in disease development. However, the main focus was on investigating a promising region on cattle chromosome (BTA) 10 (Hernandez-Sanchez et al., 2002) and the PRNP promoter region. We also aimed to identify new candidate genes by a genome-wide association approach. Of the candidate region on BTA 10, we characterised and screened a 300-kb region encompassing four genes (ARIH1, HEXA, BRUNOL6 and PARP6) for polymorphisms, which we subsequently used for an association study with BSE susceptibility. To this end, we analysed BSE affected and control animals of Holstein Friesian from the UK and Germany. Successful genotyping of 38 SNPs in the UK Holsteins (350 diseased and 270 control animals) revealed three intronic SNPs to be associated with the BSE status with permuted pvalues ranging from 5 x 10-2 to 2 x 10-3. The three SNPs are in strong linkage disequilibrium with the rare alleles contained in the so-called ‚UK-protective’ haplotype, which is significantly overrepresented in the controls with a permuted p-value of 2 x 10-3. However, we could not confirm these findings in the German Holstein animals (73 diseased and 627 controls). Albeit not significant, the protecting haplotype and alleles are over-expressed in the German Holstein BSE affected animals. We suppose that a causal mutation is in linkage disequilibrium with the investigated region and located more upstream on BTA 10. Promising results from a preliminary association study in the gene THSD4 which is located upstream of the HEXA region support this hypothesis. Furthermore, we investigated two PRNP promoter insertion/deletion polymorphisms (23-bp and 12-bp, respectively) and could demonstrate significant association with the BSE status in three of four cattle populations. Genotyping of BSE-diseased and control animals of UK Holstein (350 cases vs. 270 controls), German Holstein (127 cases vs. 627 controls), German Brown (43 cases vs. 90 controls) and German Fleckvieh (106 cases vs. 137 controls) revealed a significant overrepresentation of the deletion alleles at both polymorphic sites in diseased animals with p-values ranging from 5 x 10-2 to 6 x 10-4. The main effect on susceptibility is associated with the 12-bp indel polymorphism. Compared with non-carriers, heterozygous and homozygous carriers of the 12-bp deletion allele possess relatively higher risks of having BSE, ranging from 1.32 to 4.01 and 1.74 to 3.65 in the different breeds. We assume that 35% to 53% of the BSE cases would not have appeared if the risk allele had not existed in the different populations. These results demonstrate a substantial genetic PRNP associated component for BSE susceptibility in cattle. However, although the BSE risk conferred by the deletion allele is considerable, the main risk factor for BSE in cattle is environmental, i.e. exposure to feedstuffs contaminated with the infectious agent. Analysis of SNPs in the candidate genes LAMR1 (BTA22), PLG (BTA9), IREB2 (BTA21) and HSPA8 (BTA15) revealed no significant association with the BSE status. However, weak SNP coverage of these genes does not allow dismissing these genes from the list of potential candidate genes for BSE susceptibility. A genome-wide association study aimed to identify new candidate genes by genotyping ten thousand SNPs in a panel of BSE affected and control animals. This study is not yet completed. Preliminary results are currently indicating 18 potential candidate regions on 14 chromosomes.