• Journal of Animal Science and Technology
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• v.53 no.4
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• pp.303-310
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• 2011

Phylogenetic relationships of Jeju dogs to other domestic and foreign dog breeds were assessed using mtDNA D-loop sequences. Neighbor-joining trees were constructed using complete sequences (970 bp excluding the tandem repeat region) determined for five Cheju, four Jindo, four Sapsaree, five Pungsan, two of each East and West Laika dogs (Canis familiaris), two gray wolves (Canis lupus) and two coyotes (Canis latrans) and also published complete sequences for dogs. Coyote sequences were used as outgroups. In addition, a total of 214 haplotypes of 598bp D-loop sequences from 30 dog breeds were collected from GenBank and used to investigate genetic structure of population. In the analyses of full D-loop sequence variation and the phylogenetic trees constructed by neighbor-joining method, neither haplotypes nor clades specific for any domestic dog breeds were observed. The inter-species sequence variation (4.51%) between domestic dogs and wolves was much higher than the intra-species sequence variation within domestic dogs (1.63%) and wolves (3.64%). The divergence of the dog and wolf occurred approximately 1~2 million years ago based on these values. The taxa of Jeju dog breed in the phylogenetic tree are clustered separately and intermingled with other taxa of breeds, suggesting that active crossbreeding of Jeju dogs with other domestic breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.457-466
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• 2015

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value ($F_{IS}$) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high $F_{ST}$ values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• Journal of Species Research
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• v.13 no.2
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• pp.127-130
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• 2024

The first complete mitogenome sequence of the Red-tongue Pit Viper (Gloydius ussuriensis) from Korea was characterized using next-generation sequencing. The mitogenome is a circular molecule (17,209 bp) with a typical vertebrate mitogenome arrangement, which consists of 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), two non-coding regions (D-loop), and 13 protein-coding genes (PCGs). The base composition of the mitogenome is 32.7% of A, 27.5% of C, 13.9% of G, and 25.9% of T, with a slight AT bias(58.6%). This phylogenetic analysis infers that G. ussuriensis is in the same group as the Chinese G. ussuriensis (Accession No. KP262412) and is closely related to G. blomhoffi and other species of the genus Gloydius. In our study, the complete mitogenome sequence of Korean G. ussuriensis was characterized and we provided basic genetic information on this species.

• Journal of Animal Science and Technology
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• v.46 no.5
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• pp.735-742
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• 2004

This study was conducted for the identification of pure Landrace, Large White and Duroc breeds which are mainly maintained in Korea using DNA markers. We used known KIT and MC1R mutations, which were related coat color in pigs, and pig mitochondrial DNA variations. The KIT mutation was used to distinguish white and colored animals. Duroc breed could be discriminated from other colored breeds using the MC1R mutation N121D. Discriminating Landrace and Large White was possible using the l l-bp duplication of D-Ioop region and alternative initiation codon of ND2. In conclusion, identification of Landrace, Large White and Duroc breeds was might be possible using the procedure designed in this study.

• Parasites, Hosts and Diseases
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• v.58 no.1
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• pp.73-79
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• 2020

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

• 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.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.4
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• pp.585-588
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• 1997

The polymerase chain reaction (PCR) technique was used to distinguish from two morphologically similar red algal species; Acrosorium polyneurum and A. yendoi. Total DNA was extracted by the LiCl method. The extracted DNA (15 ng) in a $25{\mu}\ell$ reaction volume was amplified by the PCR technique using primers covering with mitochondrial D-loop gene, nuclear rDNA internal transcribed spacer (ITS), and nuclear rDNA external transcribed spacer. A. yendoi could be distinguished from A. polyneurum on the producible basis of amplified ITS fragment of 650 bp.

• Journal of Life Science
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• v.21 no.3
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• pp.385-392
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• 2011

The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.

• 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.