Automated Single-Strand Conformation Polymorphism Reveals Low Diversity of a Major Histocompatibility Complex Class II Gene in the Threatened New Zealand Sea Lion
Molecular Ecology Resources
ABI, DQB, Genetic diversity, Major Histocompatibility Complex, New Zealand sea lion, Population genetics, SSCP
Single-strand conformation polymorphism (SSCP) analysis of the second exon of the DQB gene in the endemic New Zealand sea lion (Phocarctos hookeri) was automated using fluorescently-labelled PCR primers and a capillary sequencer. SSCP mobility profiles (n = 61 individuals) were confirmed by direct sequencing of genomic polymerase chain reaction (PCR) products (n = 39). We found only two alleles defined by changes at a single codon of this apparently functional locus. SSCP at a constant temperature above ambient allowed consistent and rapid genotyping. By comparison, sequence-based genotyping was highly dependent on the threshold used to identify secondary peaks indicative of a heterozygote.
Lento, G. M.; C. S. Baker; Victor David; Naoya Yuhki; N. J. Gales; and Stephen J. O'Brien. 2003. "Automated Single-Strand Conformation Polymorphism Reveals Low Diversity of a Major Histocompatibility Complex Class II Gene in the Threatened New Zealand Sea Lion." Molecular Ecology Resources 3, (2): 346-349. https://nsuworks.nova.edu/cnso_bio_facarticles/602