The first deviation from procedures happens during the MC1R sequencing preparations. After so many PCR reactions, it is not surprising that some groups would lose their test tubes as the heat from the thermocycler erases the labels on tubes. Unfortunately, we were confident that our tubes were gone. Despite remembering the color of our labels as well as where we placed them, none of the tubes from both genetic lab sections matched our description. Loss of the MC1R PCR products resulted in us having to use Dog 5’s MC1R sequencing, which came out as below average, yet useable, quality.
In the comparison between Tasha the Boxer versus our sample dog, EMBOSS Needle showed many gaps between the reference sequence and our sequence. The gaps could be due to the poor quality that came up from the files. MC1R PCR products may not have been amplified to a great extent due to lack of dNTPs or primers. The SNP at nucleotide 790 helps conclude that our dog does not have a melanistic mask because our sequence does not have the same nucleotide (C) at 790 as the reference sequence (G). The SNP at nucleotide 808, 832, and 901 are specific to Siberian Husky dogs, which may suggest our dog is a Siberian Husky, or at least related to a breed of Siberian Husky. The relationship was no surprise because our first BLAST results showed that our MC1R sequence could be related to a Siberian Husky breed with 97.85% identity. MC1R files showed that at the MC1R gene is homozygous at nucleotide 916, which means the dog cannot be yellow because our dog must have two copies of nonfunctional MC1R (the e allele) to not produce eumelanin.