• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1547-1554
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• 2016

To assess genetic diversity and maternal origin of Turkish and Iranian native chicken breeds, we analyzed the mtDNA D-loop sequences of 222 chickens from 2 Turkish (Denizli and Gerze) and 7 Iranian (White Marandi, Black Marandi, Naked Neck, Common Breed, Lari, West Azarbaijan, and New Hampshire) native chicken breeds, together with the available reference sequences of G. gallus gallus in GenBank. The haplotype diversity was estimated as $0.24{\pm}0.01$ and $0.36{\pm}0.02$ for Turkish and Iranian populations, respectively. In total, 19 haplotypes were observed from 24 polymorphic sites in Turkish and Iranian native chicken populations. Two different clades or haplogroups (A and E) were found in Turkish and Iranian chickens. Clade A haplotypes were found only in White Marandi, Common Breed and New Hampshire populations. Clade E haplotypes, which are quite common, were observed in Turkish and Iranian populations with 18 different haplotypes, of which Turkish and Iranian chickens, Clade E, haplotype 1 (TRIRE1) was a major haplotype with the frequency of 81.5% (181/222) across all breeds. Compared to red jungle fowl, Turkish and Iranian chicken breeds are closely related to each other. These results suggest that Turkish and Iranian chickens originated from the same region, the Indian subcontinent. Our results will provide reliable basic information for mtDNA haplotypes of Turkish and Iranian chickens and for studying the origin of domestic chickens.

• Biomedical Science Letters
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• v.11 no.2
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• pp.227-235
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• 2005

It has been reported that endurance performance is influenced by various environmental and genetic factors. In view of an important role of human mitochondrial DNA (mtDNA) as a candidate for endurance performance, this study focused on the relationships between $VO_{2max}$ value as a measure of endurance performance or other associated phenotypes and four mtDNA restriction fragment length polymorphisms (RFLPs) (Bam HI, Hinc II1, Hinc II2 and Nci I) in the NADH dehydrogenase subunit 5 and one (Kpn I) in the D-loop region of mtDNA. MtDNA was purified from buffy coat in human peripheral blood, and PCR-RFLP analysis was performed to estimate the allele frequencies of each polymorphism in the mtDNA. There were no significant differences in allele distributions of all polymorphisms studied between male athletes and controls, respectively (P>0.05). However, the Kpn I polymorphism was significantly associated with diastolic blood pressure level in male athletes, respectively (P<0.05). Therefore, our results suggest that this polymorphism might be one of the factors modifying inter-individual difference in cardiovascular risk. Further studies using larger sample size will be required to generalize these results from the study described herein.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.4
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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.

• Korean Journal of Poultry Science
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• v.36 no.4
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• pp.323-328
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• 2009

In order to determine the origin and genetic diversity among chicken breeds, mitochondrial (mt) DNA D-loop sequences have been widely used. In this study, 41 individuals from four breeds (Korean native chicken (Black and Brown) and two imported breeds, Rhode Island Red and Cornish) were used for identifying genetic relationships with other chicken breeds. We obtained ten haplotypes and the highest number of haplotype was represented by eight individuals each from haplotype 1 and haplotype 2. Neighbor-joining phylogenetic tree indicates that the black and brown Korean native chicken breeds were mixed in haplotype 2 and they were closely related with the red jungle fowl (Gallus gallus). We also investigated whether the D-loop hypervariable region in chicken mtDNA can be used for the breed identification marker. The results indicated that the combination of the SNPs in the D-loop region can be possibly used for the breed discriminating markers. The results obtained in this study can be used for designing proper breeding and conservation strategies for Korean native chicken, as well as development of breed identification markers.

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.101.2-101
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• 1994

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.12
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• pp.1637-1643
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• 2011

Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1394-1398
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• 2006

The complete mtDNA D-loop regions of Japanese and Korean cattle were analyzed for their mtDNA variations and genetic relationships. Sequencing the 30 Higo substrain and 30 Tosa substrain of Japanese Brown, respectively 12 and 17 distinct Bos haplotypes were identified from 77 polymorphic nucleotide sites. In order to focus on the relationships among Japanese and Korean cattle, two types of phylogenetic tree were constructed using individual sequences; first, a neighbor-joining tree with all sequences and second, reduced median networks within each Japanese and Korean cattle group. The trees revealed that two major mtDNA haplotype groups, T3 and T4, were represented in Japanese and Korean cattle. The T4 haplogroup predominated in Japanese Black and Japanese Brown cattle (frequency of 43.3-66.7%), while the T3 haplogroup was predominant (83.3%) and T4 was represented only twice in the Korean cattle. The results suggested that the mitochondrial origins of Japanese Brown were Japanese ancient cattle as well as Japanese Black in despite of the considerable introgression of Korean and European cattle into Japanese Brown.

• Animal Bioscience
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• v.35 no.8
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• pp.1141-1150
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• 2022

Objective: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea. Methods: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software. Results: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia. Conclusion: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

• Animal Bioscience
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• v.35 no.7
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• pp.949-954
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• 2022

Objective: The present study is aimed at phenotypic characterization and mitochondrial d-loop analysis of indigenous "Diara" buffalo population, which are mostly confined to the villages on the South and North Gangetic marshy plains in the Bihar state of India. These buffaloes are well adapted and are best suited for ploughing and puddling the wet fields meant for paddy cultivation. Methods: Biometric data on 172 buffaloes were collected using a standard flexible tape measure. Animals are medium in size; the typical morphometric features are long head with a broad forehead and moderately long and erect ears. Genomic DNA was isolated from unrelated animals. The mtDNA d-loop 358-bp sequence data was generated and compared with 338 sequences belonging to riverine and swamp buffaloes. Results: Based on the mitochondrial d-loop analysis the Diara buffaloes were grouped along with the haplotypes reported for riverine buffalo. Sequence analysis revealed the presence of 7 mitochondrial D loop haplotypes with haplotype diversity of 0.9643. Five of the haplotypes were shared with established swamp breeds and with Buffalo population of Orissa in India. Conclusion: Morphometric analyses clearly shows distinguishing features like long and broad forehead which may be useful in identification. The germplasm of Diara buffalo is much adapted to the marshy banks of river Ganga and its tributaries. It constitutes a valuable genetic resource which needs to be conserved on priority basis.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.4
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• pp.531-538
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• 2020

Objective: Evidence from previous reports indicates that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River. Further research identified two new origin centers for domestic pigs in the Tibetan Plateau and the islands of Southeast Asia. However, due to the small sample size of Tibetan pigs, details of the origin and spread of Tibetan pigs has not yet been established. Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces. Comprehensive Tibetan pig samples were taken to perform the most detailed analysis of Tibetan pigs to date. Results: The result indicate that Rkaze pigs had the lowest level of diversity, while Changdu pigs had the highest diversity. Interestingly, these two populations were both in the Tibetan Plateau area. If we calculate diversity in terms of each province, the Tibetan Plateau area had the lowest diversity, while the Chinese province of Gansu had the highest diversity. Diversity gradient analysis of major haplotypes suggested three domestication centers of Tibetan pigs in the Tibetan Plateau and the Chinese provinces of Gansu and Yunnan. Conclusion: We found two new domestication centers for Tibetan pigs. One is in the Chinese province of Gansu, which lies in the upstream region of the Yellow River, and the other is in the Chinese province of Yunnan.