Single strand conformation polymorphism of PRNP exon-III region in Karnah sheep breed of India

SSCP polymorphism was detected of ovine PRNP coding region exon-3 in 50 genomic DNA samples from Karnah sheep (Ovis aries), an endangered fine wool breed of Jammu and Kashmir State in India. Patterns of nucleotide variation associated with PRNP polymorphism in exon-3 were screened using PCR-SSCP primers covering different nucleotide base pairs. Primer set-I covering 19-373 nucleotide and showed 9 haplotypes, primer set-IT covering nucleotide regions from 354-711 showed 7 haplotypes and primer set-Ill nucleotide region from 692-1001 showed 7 haplotypes. The frequency of A, B, C, D, E, F, G, H, and I haplotypes in segment-I were 6.00, 6.00, 6.00, 20.00, 36.00, 6.00, 6.00, 6.00 and 8.00% respectively. PCR-SSCP haplotypes in segment-IT, covering scrapie susceptibility/resistance codons A, B, C, D, E, F and G were in 10.00, 44.00, 18.00, 18.00,4.00,4.00 and 2.00% frequencies respectively. In third segment,PCR-SSCP variants A, B, C, D, E, F and G were in frequencies of 34.00, 18.00, 16.00, 8.00, 10.00, 6.00 and 8.00% respectively. Data generated in this study will be useful for the screening of SNP markers related to scrapie disease resistance or susceptibility in India