Genotype of Dogs

The end goal of this entire unit with dogs was to infer the genotype of the dogs at different genes. This was done by sequencing either the entire genome or, more practically, specific sequences containing desired single nucleotide polymorphisms (SNPs). There are many methods by which sequencing can be accomplished, but the most common method is Sanger sequencing. Sanger sequencing is run by amplifying desired DNA sequences in a solution containing regular deoxynucleotides (dNTPs) and a minimal amount of dideoxynucleotides (ddNTPs). These ddNTPs are structurally similar to typical nucleotides, but lack an OH group on the 3’ carbon that prevents the growth of the chain. As a result, sequences terminate at different lengths depending on the how early the ddNTP is added. The differently sized products of the amplification are then run through an agarose gel where they separate into bands. The distribution of the bands can then be used to read the sequence of the DNA. This method, while effective, can require lots of reagents and gels if more than a small sequence is being analyzed