• Asian-Australasian Journal of Animal Sciences
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• 제18권10호
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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.

• Journal of Animal Science and Technology
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• 제45권6호
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• pp.911-916
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• 2003

돼지 Duroc 품종의 mitochondria DNA D-loop전체 유전자를 증폭하기 위하여 많은 동물에서 고도로 상동성이 높은 tRNA-Pro와 tRNA-Phe 염기서열 일부를 이용하여 oligonucleotide primer를 제작하였다. 그 결과 Duroc 품종의 D-loop 전체 유전자는 1,145 base pairs 였으며, 그 중간위치에 10bp의 Sus Scrofa-specific sequence (TACACGTGCG)가 10개 존재하고 있었다. 돌연변이 검출을 위하여 가장 변이가 심한 지역을 primer 제작하여 345 bp의 DNA 단편을 증폭하였으며, Single Stranded Conformation Polymorphism(SSCP) 분석은 8% polyacrylamide gel에서 200 V, 16시간 전기영동하여 ethidium bromide (EtBr)로 10분간 염색하여 UV image analyzer로 관찰하였다. 그 결과 두 개의 서로 다른 밴드유형을 관찰하였으며, 21개 부위에서 염기서열 변이가 관찰되었다. 이러한 결과는 유전적 다양성 변이를 검출하는데 SSCP 분석이 유용한 도구라고 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제20권4호
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• pp.471-476
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• 2007

Little is known about the origin and genetic diversity of swamp buffaloes in China. To obtain more knowledge on genetics of the water buffalo in China, the complete mitochondrial D-loop sequences of 30 samples from 6 native types were investigated. The results revealed 12 mitochondrial haplotypes with 50 polymorphic sites. Among these polymorphic sites, there were 49 transitions and 1 transversion. The average nucleotide diversity and haplotype diversity estimated from mtDNA D-loop region in 6 Chinese water buffalo types were 0.00684 and 0.798, respectively, showing rather abundant mitochondrial genetic diversity. The Neighbor-Joining (NJ) tree of mtDNA of Chinese water buffaloes was constructed according to the 12 haplotypes. The NJ tree indicated two lineages being designated lineage A and lineage B, in which lineage A was predominant, and lineage B was at low frequency. The new lineage B was first discovered and defined in 6 Chinese water buffalo types. These results showed that two different maternal lineages were involved in the origin of domestic swamp buffaloes in China and the lineage B was probably an introgression from Southeast Asian buffaloes.

• Genomics & Informatics
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• 제18권3호
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• pp.32.1-32.7
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• 2020

The mitochondrial genome of a species is an essential resource for its effective conservation and phylogenetic studies. In this article, we present sequencing and characterization of the complete mitochondrial genome of a threatened labeonine fish, Cirrhinus reba collected from Khulna region of Bangladesh. The complete mitochondrial genome was 16,597 bp in size, which formed a circular double-stranded DNA molecule containing a total of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes) with two non-coding regions, an origin of light strand replication (OL) and a displacement loop (D-loop), similar structure with other fishes of Teleostei. The phylogenetic tree demonstrated its close relationship with labeonine fishes. The complete mitogenome of Cirrhinus reba (GenBank no. MN862482) showed 99.96% identity to another haplotype of Cirrhinus reba (AP013325), followed by 90.18% identity with Labeo bata (AP011198).

• BMB Reports
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• 제31권6호
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• pp.604-606
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• 1998

The nucleotide sequence of two hypervariable regions of the D-loop and the frequency of the 9-bp repeat in the region V of mitochondrial DNA (mtDNA) were investigated in the Korean population. Alignment of these sequences with the published reference revealed a unique pattern of base substitution and deletion compared with those of other races. The deletion and addition frequency of the 9-bp repeat in the region V was also distinct.

• Journal of Animal Science and Technology
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• 제44권2호
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• pp.181-190
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• 2002

본 연구는 한우 mt DNA 염기서열 가운데 $tRNA^{Pro}$와 $tRNA^{Pre}$ 유전자 사이에 위치하고 있는 D-loop 영역의 염기서열을 결정하고 한우의 염기변이 다형성을 분석하기 위하여 mt DNA의 D-loop 영역내 404번부터 15061까지 1142bp 크기의 염기서열 부위를 특이적인 primer를 이용하여 PCR로 증폭하였다. 한우의 mt DNA내 D-loop 영역에서 단일염기의 치환 및 삽입에 의해 총 24개의 polymorphic site가 확인되었다. 한우 mt DNA D-loop 영역 가운데 16042～16122번째에 위치하고 있는 영역의 염기치환율이 다른 염기서열 영역에 비하여 약 50%를 점유하고 있었으며 이들 polymorphic site에서 16055, 16230 및 16260 번의 염기치환은 한우에서만 검출된 새로운 염기변이로 확인되었다. 따라서, 한우 D-loop 영역내 특이적인 염기변이는 모계 및 세포질 DNA marker로서 한우품종을 특정하는데 활용할 수 있는 가능성을 시사하였다. Polymorphic site의 출현빈도는 169번째 염기가 81.3%로 가장 출현율이 높았고 다음으로 16302번과 16093번째는 56.3% 그리고 16042번와 16119번째 염기가 각각 50.0%와 43.8%의 치환율을 보였으며 나머지 14개 염기는 6.3%에서 25.0% 수준의 출현율을 나타냈다. 한우와 타 품종간의 유전적 근연관계를 추정한 결과 Bos taurus 계통의 유럽종과 유전적 유사도가 높은 것으로 추정되었고, Africa와 India의 Bos indicus 계통의 품종과는 상대적으로 근연관계가 먼 것으로 나타났다. 본 연구에서 검출한 mt DNA내 D-loop 영역의 염기서열 다형성은 한우집단의 유전적 변이성 추정과 모계유전 분석 및 나아가 경제적으로 중요한 형질들과의 연관성 분석에 유용하게 활용할 수 있을 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제24권2호
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• pp.155-161
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• 2011

In this study, mitochondrial DNA (mtDNA) sequence polymorphism was used to assess genetic diversity of nine Vietnamese local chicken breeds. In addition, two Chinese breeds kept in Vietnam were included in the analysis for comparison. A 455-bp fragment of the mtDNA D-loop region was sequenced in 222 chickens of these 11 breeds. As reference, a skeleton was constructed based on chicken mtDNA sequences taken from the Genbank. Haplotypes of the nine Vietnamese local and two Chinese breeds were aligned together with these sequences. The Vietnamese and Chinese breeds showed a high degree of variability. In total, 37 haplotypes were identified in the chicken breeds studied forming eight clades. Thereby, the majority of individuals of the two Chinese breeds grouped together in one clade which is assumed to have its roots in the Indian subcontinent. Although the Vietnamese chicken breeds were distributed across all eight clades, most of them clustered in three main clades. These results suggest that the Vietnamese domestic chickens have originated from multiple maternal lineages, presumably from Yunnan and adjacent areas in China, South and Southwest China and/or surrounding regions (i.e. Vietnam, Burma, Thailand, and India).

• 생명과학회지
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• 제19권4호
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• pp.467-471
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• 2009

돼지 6품종(Landrace, Duroc, Large White, 한국재래돼지, Berkshire, Hampshire)을 대상으로 기존에 보고된 서열을 바탕으로 제작한 primer를 이용하여 mtDNA D-loop 전체영역을 증폭하였다. 증폭된 PCR product를 cloning 및 DNA sequencing, 다중염기서열비교를 통하여 분석한 결과, mtDNA에서 heteroplasmy가 나타나는 D-loop 내 tandem repeat region 이후에 11-bp 중복이 존재하는 것을 확인하였다. 이런 중복현상은 일본재래돼지와 Duroc에서 보고되었지만, 이를 이용한 돼지 품종별 중복현상의 빈도 및 분포에 관한 연구는 이루어져있지 않다. 품종별 11-bp 중복현상을 분석하기 위해서 6품종을 대상으로 중복지역을 포함한 약 150 bp 절편을 증폭하였으며, PAGE 방법을 통하여 분석하였다. 그 결과 본 연구에서 사용한 품종들 중 모든 Large White에서 중복현상이 발생하는 것을 확인하였으며, Duroc인 경우 11.2% (9/80)에서 중복현상이 확인되었다. 반면에 Landrace, 한국재래돼지, Berkshire 및 Hampshire에서는 전혀 발견되지 않았다. 이런 결과로서, 11-bp 중복현상의 분석은 현재 구별이 불가능한 Landrace와 Large White를 구별할 수 있는 유용한 DNA marker로서 사용이 가능할 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권6호
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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.

• Archives of Pharmacal Research
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• 제29권1호
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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.