Intra‐ and interbreed genetic variations of mitochondrial DNA major non‐coding regions in Japanese native dog breeds [Canis familiaris)

Abstract

Mitochondria1 DNA (mtDNA) major non-coding regions were amplified from 73 dogs of eight Japanese native dog breeds and from 2 1 dogs of 16 non-Japanese dog breeds by the polymerase chain reaction and their DNA sequences were determined. A total of 51 nucleotide positions within the non-coding region (969-972 base pairs) showed nucleotide variations of which 48 were caused by transition. These nucleotide substitutions were abundant in the region proximate to tRNAPr0. In addition to the nucleotide substitutions, the dog mtDNA D-loop sequences had a heteroplasmic repetitive sequence (TACACGTCCG) involving size variation. The DNA sequences of the non-coding region were classified into four different groups by phylogenetic analysis and the deepest branchpoints of this dog phylogeny was calculated to about 100 000 years before the present. Phylogenetic analysis showed that Japanese native dog breeds could not be clearly delimited as distinct breeds. Many haplotypes found in members of some clustering groups were seen in each dog breed, and interbreed nucleotide differences between Japanese dog breeds were almost the same as the intrabreed nucleotide diversities.

Molecular characterization of the canine mitochondrial DNA control region for forensic applications

“…The ternary site 15639 brought mutations in a total of 28 hgs (87.5%), where a transversion to A was observed in 20 hgs (62.5%) and a transversion to G in 8 hgs (25%). The positions located in HVS-I were also found to be highly polymorphic in previous studies [12,14,[22][23][24], partly using other nomenclatures for base designation (Table S3). In Angleby and Savolainen [14], position 15627 showed a mutation in 49 hgs (39.5%), position 15639 in 109 hgs (88%; 73 hgs [59%] harboured the variant A, 36 hgs [29%] showed a G) and position 15955 displayed a mutation in 48 hgs (39%); in Savolainen et al [24], position 15627 showed a G in 75 hgs (48%) and even one transversion (A-T, W11), position 15639 displayed a mutation in 139 hgs (90%), where 106 hgs (68%) showed an A and 33 hgs showed a G (21%), of which two had a deletion at this position, and position 15955 showed a mutation in 51 hgs (33%).…”

“…In agreement with [21], the importance of a unique standardized reference sequence is also emphasized here, as the application of different reference sequences confuses the reporting of mtDNA haplotypes [12,15,20,[22][23][24]28]. Table S3 presents some different notations of already established data in a comparative way [12,20,22,23] to help harmonization of results.…”

“…As already stated in [21], most laboratories analyse HVS-I as a segment ranging between positions 15458 and 16039, with the exception of [22,28] who also sequenced HVS-II. As the repeat region starts at position 16130, sequence information within a string of 90 nucleotides is missed when the commonly used sequencing strategy is applied.…”

“…Among others, this would involve positions 16083 (A-G) and 16128 (G-A), which showed a high degree of variability ( Fig. 1, Table S2 and [22]). …”

“…Table S3 presents some different notations of already established data in a comparative way [12,20,22,23] to help harmonization of results.…”