• Animal Systematics, Evolution and Diversity
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• 제24권1호
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• pp.25-32
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• 2008

The Gold-spotted pond frog, Rana plancyi chosenica, designated as a vulnerable species by IUCN Red list. This species is a typical example facing local population threats and extinction due to human activities in South Korea. A strategic conservation plan for this endangered species is urgently needed. In order to provide information for future conservation planning, accurate information on the genetic diversity and taxonomic status is needed for the establishment of conservation units for this species. In this study, we used a molecular genetic approach using the mitochondrial cytochrome b gene and control region sequences to find the genetic diversity of gold-spotted pond frogs within South Korea. We sequenced the mitochondrial DNA cytochrome b gene and control region of 77 individuals from 11 populations in South Korea, and one from Chongqing, China. A total of 15 cytochrome b gene haplotypes and 34 control region haplotypes were identified from Korean gold-spotted pond frogs. Mean sequence diversity among Korean gold-spotted pond frogs was 0.31% (0.0-0.8%) and 0.51% (0.0-1.0%), respectively. Most Korean populations had at least one unique haplotype for each locus. The Taean, Ansan and Cheongwon populations had no haplotypes shared with other populations. There was a sequence divergence between Korean and Chinese gold-spotted pond frogs (1.3% for cyt b; 2.9% for control region). Analysis of genetic distances and phylogenetic trees based on both cytochrome b and control region sequences indicate that the Korean gold-spotted pond frog are genetically differentiated from those in China.

• 한국조류학회지
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• 제25권2호
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• pp.106-111
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• 2018

괭이갈매기는 동북아시아에서 가장 흔한 갈매기류 중 하나이며, IUCN에 의하면 LC(Least Concern)로 분류되어 있다. 인간의 활동이 해양환경에 영향을 미친 이래 괭이갈매기는 해양 환경오염과 서식지 교란의 중요한 지표종이 되었다. 본 연구에서 괭이갈매기가 6개의 미토콘드리아 CO1 하플로타입(haplotype)이 있고, 이중 일부 희귀 haplotype은 지리적으로 제한되어 나타난다는 사실을 확인하였으며, 이러한 현상은 본 종이 멀리 분산하지 않음을 암시한다. 본 논문은 한국에서 괭이갈매기를 대상으로 한 첫번째 개체군 유전적 연구결과이며, 환경지표종으로서 모니터링과 유전학적 연구의 기초자료가 될 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권4호
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• pp.501-507
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• 2019

Objective: The Agu is the only native pig breed in Japan, which is reared in Okinawa prefecture, the southernmost region in Japan. Its origins are considered to be of Asian lineage; however, the genetic background of the Agu is still unclear. The objective of this study was to elucidate the maternal lineage of the Okinawa indigenous Agu pig with the use of the mitochondrial DNA (mtDNA) control region. Methods: The mtDNA control regions of Agu pigs were sequenced and the phylogenetic relationship among Agu, East Asian and European pigs was investigated with the use of 78 Agu individuals. Results: Twenty-seven polymorphic sites and five different haplotypes (type 1 to type 5) were identified within the Agu population. Phylogenetic analysis indicated that types 1 and 2 were included in East Asian lineages; however, the remaining types 3, 4, and 5 were of European lineages, which showed a gene flow from European pigs in the 20th century. Sixty-seven out of 78 Agu individuals (85.9%) possessed mtDNA haplotypes 1 and 2 of the East Asian lineage, which were identical to two haplotypes of ancient mtDNA (7,200 to 1,700 years before the present) excavated at archaeological sites in Okinawa. Conclusion: This study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.

• Animal Bioscience
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• 제35권6호
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• pp.826-837
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• 2022

Objective: Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods: A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results: A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion: Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

• 대한의생명과학회지
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• 제29권4호
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• pp.302-313
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• 2023

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex^® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10^-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10^-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

• Clinical and Experimental Pediatrics
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• 제48권5호
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• pp.495-499
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• 2005

목 적 : IL-4는 Th2 면역 반응의 중요한 매개체로 IL4 유전자의 promoter 일배체형(haplotype)은 한국인 소아에서 RSV에 의한 심한 모세기관지염과 연관된다고 알려져 있다. 본 연구는 IL4 유전자의 promoter 다형성에 따른 IL-4 단백의 기능적인 변화를 분석하여 심한 RSV 하기도 감염증에 기여하는 IL4 유전자의 발병 기전의 연관성을 연구하고자 시행하였다. 방 법 : 면역 기능이 정상인 소아 20명을 대상으로 전혈을 채취한 후 genomic DNA를 추출하여 IL4 유전자 promoter 약 1.2 kb 부위를 증폭시켰다. 염기서열 분석을 통하여 IL4 유전자 promoter의 유전형을 결정하고, PHASE 분석으로 일배체형을 결정하였다. 각 일배체형별로 $5{\mu}g$의 DNA를 Jurkat T 세포에 핵형질변환 시켜서 정상 Jurkat T 세포와 PMA(50 ng/mL)로 자극한 세포에서의 luciferase 활성도를 분석하여 IL4 유전자 promoter의 전사능을 결정하였다. 결 과 : 한국인 소아의 일배체형은 3가지 유형 GCC(7%), TCC(17%), 및 TTT(76%)로 분포하였다. Jurkat T 세포의 절대 luciferase 활성도는 GCC형이 가장 낮았고 TTT형이 가장 높았다. GCC 일배체형을 기준으로 하여 나타낸 Jurkat T 세포의 상대 luciferase 활성도는 TCC형이 4.2배, TTT형이 5.3배로 증가되었다. PMA로 자극한 후에 측정한 각 일배체형의 luciferase 활성도 역시 GCC형에 비하여 TCC형이 3.0배, TTT형이 4.1배로 증가되어 자극하지 않은 세포에서와 유사한 활성도의 차이를 보였다. 결 론 : 소아의 심한 RSV 하기도 감염증과 연관된 IL4 유전자의 promoter 일배체형 TTT는 IL4 유전자의 promoter의 전사능을 증가시킴으로써 영아 및 소아의 RSV 하기도 감염증의 병인에 중요한 역할을 할 것으로 생각된다.

• 한국산림과학회지
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• 제94권3호통권160호
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• pp.178-182
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• 2005

소나무의 2년생 인공교배(人工交配) 전형매차대목(全兄妹次代木) 114개체를 대상으로 화분친(花粉親)이 아닌 개체의 화분에 의해 생성된 차대목(次代木)을 식별하기 위하여 부계유전(父系遺傳)되는 반수체(半數體) 표지자인 cpSSR 표지자 분석을 실시하였다. 3개의 cpSSR primer를 이용한 PCR 분석을 통하여 화분친(花粉親)과 3개 모수(母樹)의 haplotype 조합을 결정하고, 이에 의해 각 개체의 DNA 지문이 확인되었다. 동일한 cpSSR primer를 사용하여 전형매차대(全兄妹次代) 114개 개체목의 haplotype을 확인하고 이를 화분친(花粉親) 및 3개 모수(母樹)에서 확인된 haplotype 조합과 비교한 결과, 이들 중 14개체에서 인공교배(人工交配) 화분친(花粉親)과 다른 cpDNA haplotype이 확인되어 이들이 교배에 사용된 화분친(花粉親)이 아닌 타개체로부터 유입된 화분에 의해서 생성된 개체로 동정되었다. 특히, 강원30으로부터 생산된 차대(次代) 중 한 개체목은 불완전한 제웅(除雄)이나 인공교배(人工交配)시 모수(母樹)에서 생산된 화분의 유입으로 인해서 야기된 자가교배(自家交配)에 의해서 생성되었을 가능성이 매우 높은 것으로 나타났다. 본 연구에서 분석된 cpSSR 지문분석은 향후 자연림내 친계차대목(親系次代木) 감별과 삽목, 접목 및 조직배양에 의한 무성번식묘(無性繁殖苗)의 동정, 순수(純粹) 전형매차대(全兄妹次代)의 확인 등 식물법의학적(植物法醫學的) 분석법(分析法)에 유용하게 활용될 수 있을 것으로 기대된다.

• IMMUNE NETWORK
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• 제3권2호
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• pp.103-109
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• 2003

Background: As all HLA class II genes, the DQ genes show their polymorphic variation mainly in the second exon, which encodes the first extracellular domain of the molecule. PCR-SSOP (Polymerase chain reaction-Sequence specific oligonucleotide probe) techniques were frequently used for HLA-DQA1 and DQB1 typing but certain alleles, $DQA1^*0101/0104/0105$, $^*302/0303$, $*0501/0505$ and $DQB1^*0201/^*0202$ which differ from each other in segment other than exon 2, could not be unequivocally assigned. Methods: To overcome this problem, we applied additional PCR-SSP (PCR-Sequence specific primer) method to analyze DQA1 exons 1, 3 and 4 and DQB1 exon 3. And we investigated the distributions and haplotypes of HLA-DRB1, DQA1 and DQB1 alleles in 406 unrelated Korean healthy individuals. Results: Using this method the indistinguishable alleles of DQA1 and DQB1 in PCR-SSOP were typed definitively. We also found several important associations between DQA1 and DQB1 alleles in the Korean population; $DQA1^*0101-DQB1^*0501$, $DQA1^*0104-DQB1^*0502$ or $-^*0503$, $DQA1^*0105-DQB1^*0501$, $DQA1^*0302-DQB1^*0303$, $DQA1^*0303-DQB1^*0401$ or $-^*0402$, $DQA1^*0501-DQB1^*0201$, $DQA1^*0505-DQB1^*0301$, and $DQA1^*0201-DQB1^*0202$. The haplotypes of DRB1-DQA1-DQB1 associated with $DQA1^*01$, $^*03$, $^*05$, and $DQB1^*02$ subtypes were investigated. Several haplotypes associated with these alleles were observed in the Korean population. Conclusion: Our results can be helpful to find potential unrelated donors for bone marrow registries and study the HLA-associated disease and anthropology at high-resolution allelic level.

• Molecules and Cells
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• 제26권6호
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• pp.566-575
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• 2008

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

• Animal cells and systems
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• 제16권5호
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• pp.408-414
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• 2012

To reexamine taxonomic status of endemic Mogera wogura coreana from Korea, we first obtained partial 12S rRNA sequences (893 bp) and complete cytochrome b gene sequences (1140 bp) of this subspecies, and these sequences and partial cytochrome b sequences (402 bp) were compared to the corresponding haplotypes of M. wogura from East Asia, obtained from GenBank. The one of three 12S rRNA haplotypes in M. w. coreana was identical to one 12S rRNA haplotype of M. w. robusta from East Asia: 10 complete and 13 partial cytochrome b haplotypes of M. w. coreana formed a single clade with one complete and four partial cytochrome b haplotypes of M. w. robusta, respectively. We considered that M. w. coreana from Korea is an endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of M. w. coreana. Additionally, in the 12S rRNA and complete cytochrome b sequences, M. wogura from Japan was distinct from the two continental subspecies of M. w. coreana and M. w. robusta with average distances of 1.76 and 5.65%, respectively; insular M. wogura, with within-group distances of 2.09 and 4.38%, respectively, was also genetically more divergent than the mainland M. wogura, with within-group distances of 0.08 and 0.57%, respectively. Thus, we considered that insular M. wogura of Japan dispersed into neighboring East Asian continent, which is opposite to the traditional hypothesis on the origin of Japanese M. wogura.