SSCP analysis in the D-loop region of porcine mitochondrial DNA as confirmed by sequence diversity

Sequence polymorphism of the displacement loop (D-loop) region in mitochondrial DNA (mtDNA) is a cytoplasmic DNA marker. Since the analysis of single-strand conformation polymorphism (SSCP) has been used for detection of substitutions in nucleotide sequence, this technique was employed to investigate the porcine sequence polymorphism in the D-loop region. The primers were prepared to amplify the most polymorphic site with 392-bp in the D-loop region from whole blood of pigs. The PCR-SSCP patterns were identical in European breeds Landrace and Duroc, but were different in Yorkshire and in Taiwanese breeds Lanyu and Taoyuan. Nucleotide sequence analysis in the 392-bp PCR products were completely in accordance with the PCR-SSCP patterns. There was only a single nucleotide substitution between Yorkshire and Landrace/Duroc pig and 2-3 nucleotide substitutions (dependent on the breed and individual) between Taiwanese Lanyu and Taoyuan. As many as 10-11 nucleotides were different between European and Taiwanese breeds in which most differences clustered within a certain region in the D-loop. The results suggest that PCR-SSCP analysis may be used for detecting single nucleotide substitution in the porcine mtDNA D-loop region and show the diversified sequence in this region between European and Asian origins.