A SspI PCR-RFLP detecting a silent allele at the goat CSN2 locus

The comparison between the cDNA sequence obtained and the published sequences of the goat CSN2 alleles showed a new single nucleotide polymorphism (SNP) (transition C-T) at the 180th nucleotide of the ninth exon. This mutation, which took place at 124 nt from the polyadenylation site, identifies a silent allele at the CSN2 locus named CSN2 A1. Since the 9th exon C-T transition creates a SspI endonuclease restriction site, the SspI digestion of a PCR product of 360 bp spanning the 9th exon and flanking regions, would allow carriers for the presence of thymine to be identified. The allelic frequency of the CSN2 A1 allele, determined in 170 goats belonging to an undefined genetic type reared in the province of Naples (Italy), was 0.23 It has been observed that the sequences in the 3’ untranslated regions (UTR), proximal to the polyadenylation site, can affect the mechanism of mRNA deadenylation and degradation. Therefore, it is reasonable to hypothesize that the C-T transition might, directly or indirectly, influence the stability of the mRNA and, consequently, the amount of protein produced.