• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.911-916
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• 2003

The mitochondrial DNA(mtDNA) D-loop region was amplified from Duroc(Sus scrofa) by polymerase chain reaction(PCR). The oligonucleotide primer used to amplify the Sus scrofa mtDNA D-loop region was designed using tRNA-Pro and tRNA-Phe sequence in mtDNA regions highly conserved in many other animal species. There were 1,145 base pairs(bp) in the D-loop region. The middle of the region contained 10 tandem repeat of an 10-bp Sus scrofa-specific sequence, TACACGTGCG. We designed primers for PCR-mediated single stranded conformation polymorphism(SSCP) analysis that amplified a 345 bp fragment, which contained the most variable region according to our sequencing data. SSCP analysis of denatured amplification products was carried out by polyacrylamide(8%) gel electrophoresis followed by ethidium bromide staining. The SSCP analysis identified two band patterns(A and B) and comparision of these two nucleotide sequences identified 21 base substitutions. These results show that SSCP analysis of the D-loop region is useful for detecting the genetic polymorphism.

• Archives of Pharmacal Research
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• v.29 no.1
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• pp.88-95
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• 2006

Analysis of molecular nature of mitochondrial DNA (mtDNA) could be powerful marker for anthropological studies of modern populations. While population genetic studies on mtDNA have been reported for several ethnic groups, no such study has been documented for the Korean population. We surveyed mtDNA polymorphisms in the HVS I of noncoding D-loop region and its upstream region from 430 unrelated healthy Korean population by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing analysis. PCR product with 2,790 bp spanning the specific mtDNA region (mt13715-16504) was subjected to RFLP analysis using 6 restriction enzyme (Hinf I, Hae III, Alu I, Dde I, Mbo I, Rsa I). On the PAUP analysis of PCR-RFLP results, 38 mtDNA haplotypes (Hap 1-38) were detected in the Korean populations, which were classified into 11 haplogroups (Grp 1-11) of related haplotypes encompassing all 38 haplotypes. In comparison of sequencing data with Anderson's reference sequence, the transition type was more prevalent than the transversion type. Insertions or deletions were not found. In addition, three of the polymorphic sites (A16240C, A16351G, G16384A) in HVS-I region are determined newly. The polymorphic sites were distributed randomly in the region, though the frequency at each site was variable. Thus, this research might be required for the genealogical study of Orientals.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1696-1702
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• 2008

In order to learn the origin of the Chinese Mongolian horse, we analyzed polymorphisms within the mtDNA D-loop variable region in 305 horses of 6 types of 3 different breeds, including one imported breed, one cultivated breed and 4 types of one local breed. We detected 13 different haplotypes, and subsequent sequence analysis showed that all 6 horse types were genetically diverse. By constructing a cladogram of mtDNA D-loop sequences from the 6 horse types along with homologous sequences from several other horse types obtained from GenBank, we showed that Chinese Mongolian horses have a close genetic relationship with other horse types from Mongolia. We also speculate that several Chinese Mongolian horses descended from Przewalskii horse. Additionally, the 13 haplotypes were dispersed throughout the cladogram, suggesting that Chinese Mongolian horses likely originated from multiple female ancestors. A phylogenetic map of the 6 horse types showed that the genetic relationship between the local Wuzhumuqin and Wushen types were the closest. The Xinihe and Baerhu were also closely related to each other, and slightly more distantly related to the cultivated Sanhe breed. All five of the local Chinese horse types had a much more distant relationship with the imported Thoroughbred breed.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.10
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• pp.1368-1374
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• 2005

To investigate the genetic relationships among various cattle breeds, bovine mtDNA D-loop region was used in 411 animals of 18 cattle breeds, including 8 Asian Bos taurus, 7 European Bos taurus, 1 Asian Bos indicus, and 2 African Bos indicus. The size of amplified PCR products from mtDNA D-loop region was 964 bp and the products were digested by 15 different restriction enzymes. Two different band patterns were identified in eight restriction enzymes (BstXI, Hae III, Msp I, Apa I, Taq I, Alu I, BamH I, EcoN I) and the rest of restriction enzymes showed more than 3 different band patterns among which Apo I and MspR9 resulted in 7 different restriction patterns. The genotypes, number of haplotype, effective number of haplotype, and degree of heterozygosity were analyzed. Based on all the PCR-RFLP data, different haplotypes were constructed and analyzed for calculating genetic distances between these breeds using Nei's unbiased method and constructing a phylogenetic tree.

• Food Science of Animal Resources
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• v.28 no.3
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• pp.276-282
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• 2008

It is estimated that over 80% of deer antlers produced in the world are consumed in Korea. However, mislabeling or fraudulent replacement of costly antlers with cheaper ones is one of the most common problems in the domestic antler market. Therefore, there is a great need for the development of technology to identify species of antlers. This study was carried out to develop an accurate and reliable method for the identification and authentication of species or subspecies of antlers using DNA sequence analysis and comparison of mitochondrial cytochrome band D-loop region genes among antlers of five deer species, Cervus elaphus sibericus, Cervus elaphus canadensis, Cervus nippon, Cervus elaphus bactrianus and Rangifer tarandus. A variable region of cytochrome band D-loop genes was amplified using PCR with specifically designed primers and sequenced directly. The cytochrome band D-loop region genes showed different DNA sequences between the species of antlers and thus it is possible to differentiate between species on the basis of sequence variation. To distinguish between reindeer (Rangifer tarandus) antlers and other deer antlers, PCR amplicons of the cytochrome b gene were digested with the restriction enzymes NlaIV and TaqI, respectively, which generates a species-specific DNA profile of the reindeer. In addition, samples of 32 sliced antlers labeled Cervus elaphus sibericus from commercial markets were collected randomly and the mt DNA D-loop region of these antler samples was sequenced. Among the antler samples investigated, only 62.5% were from Cervus elaphus sibericus, and others were from Cervus elaphus bactrianus (25.0%), elk (Cervus elaphus canadensis) and reindeer (Rangifer tarandus). Our results suggest that DNA sequencing of mt DNA and PCR-RFLP methods using NlaIV and TaqI enzymes are useful for the identification and discrimination of deer antler species by routine analysis.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.313-315
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• 2007

Seventeen haplotypes were detected from the complete mitochondrial DNA control region sequences analyzed from eighty individuals of two Tibetan domestic sheep breeds. The nucleotide composition of all the sequences was 33.0% A, 29.7%T, 22.9%C and 14.4%G; G+C was 37.3%. The length of the sequences ranged from 1,107 bp to 1,259 bp. The difference between them was primarily due to 3-5 copy numbers of a 75 bp tandem repeat sequence. The NJ phylogenetic tree (the number of replications of bootstrap test is 1,000) presented three major domestic sheep lineages, which suggested that modern Tibetan sheep breeds are derived from three maternal sources.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.804-811
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• 2018

Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.1
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• pp.19-23
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• 2014

Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were $0.85536{\pm}0.0172$ and $0.010158{\pm}0.005555$, respectively. Although the Laotian native fowls were distributed across five clades, most of them were clustered in two main clades (A and B), which were originated in China. The other haplotypes were contained in clades D, F, and I, which originated from continental southeast Asia. These results suggest that multiple maternal lineages were involved in the origin of domestic chicken in Laos. Moreover, there appear to be at least two maternal lineages, one from China and the other from the southeast Asian continent.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.7
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• pp.955-961
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• 2009

The aim of this study was to determine the specific polymorphic sites in cattle breeds and inter- and interbreed genetic variation among breeds and to develop a databank of Turkish native cattle mtDNA using sequence analysis. The entire D-loop region was analyzed based on DNA sequences in Turkish Grey, East Anatolian Red, South Anatolian Red, and Anatolian Black native breeds. In total, 68 nucleotide differences were observed at 26 different sites. The variable positions consisted of 22 transitions, two transversions, and two insertions, but no deletions. Haplotype number, haplotype diversity, nucleotide diversity, and mean number of pairwise difference values were found to be 17, 0.993, 0.00478, and 4.275, respectively. In addition, a phylogeny was developed by comparison among cattle populations for which the entire D-loop sequence was available. A high level of genetic variation was observed within and among the native cattle breeds.

• Journal of Life Science
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• v.21 no.9
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• pp.1329-1335
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• 2011

Korean native goats, which are characterized by black coat color, have existed on the Korean peninsula for a long time. Until now, there has been no comprehensive investigation concerning their genetic diversity, phylogenetic analysis or origin. In this study, we investigated the genetic diversity and verified phylogenetic status of the Korean native goat using the 453-bp fragment of the hypervariable fragment I (HVI) of mitochondrial DNA (mtDNA) D-loop region from 60 individuals among 5 populations. The Korean native goat showed less haplotype diversity when compared with goats from other countries. In addition, 6 haplotypes that had not been previously reported were verified in this study. In phylogenetic analyses with other country's goats, 10 haplotypes from Korean native goats were classified into mtDNA lineage A. Moreover, in a phylogenetic tree for goats which contained mtDNA lineage A, 8 of 10 haplotypes could be included in a subgroup with goats from Vietnam and an area of China. However, none of the remaining haplotypes belonged to a major group of Korean native goats and were located on different independent positions. These results suggest that almost Korean native goats aligned more closely to China and Vietnam breeds in mtDNA lineage A and there was no gene flow from other mtDNA lineages. Our results will contribute to conservation strategies and genetic breeding of Korean native goats.