Mitochondrial DNA Analysis of the Domestic Dog: Control Region Variation Within and Among Breeds

Abstract

The mitochondrial DNA (mtDNA) control regions of 125 domestic dogs (Canis familiaris) encompassing 43 breeds, as well as one coyote and two wolves were sequenced and subsequently examined for sequence variation in an effort to construct a reference dog mtDNA data set for forensic analysis. Forty informative variable sites were identified that described 45 haplotypes, 29 of which were observed only once. Substantial variation was found both within and among breeds in the mtDNA derived from tissue, indicating that analysis of the mtDNA derived from dog hairs could be a valuable, discriminating piece of evidence in forensic investigations. The dog data set single nucleotide polymorphisms (SNPs) ranged from having one to six changes on a phylogenetic tree. On average, there were 1.9 character changes for each variable position on the tree. The most variable sites (with four or more changes each, listed from the most changes to the fewest) observed were 15,639 (L 5 6), 16,672 (L 5 5), 15,955 (L 5 4), 15,627 (L 5 3), 16,431 (L 5 3), and 16,439 (L 5 3). These sites were consistent with other reports on variable positions in the dog mtDNA genome. A total of 26 SNPs were chosen to best identify all major clusters in the domestic dog data set. The descriptive analyses revealed that this data set is similar to other published canine data sets and further demonstrates that this domestic dog data set is a useful resource for forensic applications. This reference data set has been compiled and validated against the published dog genetic literature with an aim to aid forensic investigations that seek to incorporate mtDNA sequences and SNPs from trace evidence such as dog hair.

Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids (Canis, Canidae)

“…This is also the case for the Northern and Southern elephant seal species, in which the sequence composition, arrangement and copy number variation of the repeats differ considerably within and between lineages (Hoelzel, 1993). However, we found different repeat numbers in the same length of the D-loop, and even in the same breed there were different lengths of D-loop regions and different numbers of repeat units, which is consistent with the report of Gundry et al (2007).…”

“…There are large differences in the lengths of the D-loop regions among the mitochondrial genomes of Canids, ranging Li, Li, Zhao, Xie and Xu from 1157 to 1353 bp (Gundry et al, 2007). The lengths of the control regions are different because of the varying numbers of repetitive motifs.…”

Mitochondrial DNA analysis of the domestic dogs in Turkey

“…The results were compared with the reference sequence of Canis familiaris published in 1998 by Kim et al [10], and the profiling step was thus completed. These results are consistent with our study and the polymorphisms of mtDNA in the positions 15 16,658 (13.71%), and 16,676 (4.03%) of the region HV-II were determined for the first time. The polymorphisms identified in our study as being specific to breeds are consistent with the polymorphisms specified by Bekaert et al in their published study [14].…”

Complex population structure in African village dogs and its implications for inferring dog domestication history

“…Village dog populations had higher levels of diversity than purebred dogs across all markers (see (17) for purebred mtDNA diversity estimates), although for SNP markers, non-native/admixed dogs had even higher diversity estimates. The high heterozygosity found in breed-admixed dogs is likely because of SNP ascertainment; by preferentially genotyping SNPs that are highly polymorphic in breed dogs, inferences based on SNP diversity in village dogs may be biased.…”