• Molecules and Cells
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• 제39권12호
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• pp.862-868
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• 2016

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and cross-bred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

• International Journal of Industrial Entomology and Biomaterials
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• 제23권1호
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• pp.155-166
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• 2011

The leaf beetle, $Chrysolina$ $aurichalcea$ (Coleoptera: Chysomelidae), is a pest damaging plants of Compositae. In order to understand the genetic diversity and geographic variation we sequenced a portion of mitochondrial COI gene (658 bp) and complete nuclear internal transcribed spacer 2 (ITS2) of the species collected from seven Korean localities. A total of 17 haplotypes (CACOI01~CACOI17), with the maximum sequence divergence of 3.04% (20 bp) were obtained from COI gene sequence, whereas 16 sequence types (ITS2CA01~ITS2CA16), with the maximum sequence divergence of 2.013% (9 bp) were obtained from ITS2, indicating substantially larger sequence divergence in COI gene sequence. Phylogenetically, the COI gene provided two haplotype groups with a high nodal support (${\geq}87%$), whereas ITS2 provided only one sequence type group with a high nodal support (${\geq}92%$). The result of COI gene sequence may suggest the presence of historical biogeographic barriers that bolstered genetic subdivision in the species. Different grouping pattern between COI gene and ITS2 sequences were interpreted in terms of recent dispersal, reflected in the ITS2 sequence. Finding of unique haplotypes and sequence types only from Beakryeng-Islet population was interpreted as an intact remnant of ancient polymorphism. As more samples are analyzed using further hyper-variable marker, further fruitful inference on the geographic contour of the species might be available.

• 한국수산과학회지
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• 제56권5호
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• pp.701-707
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• 2023

We investigated Euphausia pacifica population in Korean waters in 2016 By samplings for genetic structur at five stations. Three sampling stations were located in the middle of the water masses which were clustered by temperature and salinity whereas the other stations were at the boundaries of the water masses. We amplified a 566 bp region and compared it with sequences of E. pacifica distributed in other waters. Sequences were classified two clades, and a clade was formed in the station E. Genetic distance of station E was close to E. pacifica present in Bering Sea, while it was distant to E. pacifica present in Yellow Sea near China. In genetic analysis, seven haplotypes were formed. Hap-1 and Hap-2 were shared in all five stations, while Hap-3 was shared in station W and WS. Four independent haplotypes were present in station E. Haplotype and nucleotide diversity were the highest in station E and the lowest in station S. The F_ST distances between station E and other stations were the highest, but distances among other stations were low. As a result, we concluded that E. pacifica, which is distributed in Korean waters, has a genetic population differentiation in the East Sea (station E).

• 생명과학회지
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• 제25권11호
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• pp.1204-1213
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• 2015

도루묵은 우리나라 동해에서 어획되는 상업적으로 중요한 수산자원으로 동해안의 자원회복관리 대상어종이며, 자원량의 회복 및 보전과 관리가 필요한 어종이다. 하지만 우리나라 도루묵 자원의 관리를 위한 유전학적 분석에 따른 연구는 매우 미비한 실정이다. 따라서 본 연구는 mitochondrial DNA의 Cytochrome b (Cyt b) 유전자 서열과 5개의 microsatellite marker의 유전자형을 토대로 우리나라 동해안 도루묵과 일본 도루묵의 유전적 다양성과 집단 구조를 분석하여 유전학적 유연관계를 파악하고, 도루묵 자원의 보전과 관리를 위한 과학적 자료를 제공하기 위해 실시하였다. 한국 3개 지역(독도, 동해, 감포)과 일본의 2개 지역(북해도와 에리모)에서 채집된 총 83개 개체의 mtDNA Cyt b 영역을 분석하여 27개의 haplotype을 확인하였다. 유전적 다양성은 에리모에서 가장 높고 감포에서 가장 낮았다. Pairwise F_ST값과 유전적 거리, UPGMA와 주성분분석, AMOVA test 및 structure 분석 결과, 한국의 동해안 도루묵 집단 간 유전적 차이는 거의 없었으나 일본 도루묵 집단과는 유의적인 차이가 나타났으며(p<0.05), 한국의 동해안 집단과 일본의 집단으로 그룹을 형성하며 구분되는 유연관계를 확인하였다. 본 연구에서 확인된 도루묵의 유전적 특성 및 집단 간 유연관계는 중요한 수산유전자원으로서의 도루묵에 대한 중요한 과학적인 근거자료가 될 것이며, 앞으로 도루묵의 보존, 평가 및 이용에 활용 가능한 정보를 제공할 것이라 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권6호
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• pp.763-770
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• 2015

Improved meat quality and greater muscle yield are highly sought after in high-quality chicken breeding programs. Past studies indicated that polymorphisms of the Perilipin gene (PLIN1) are highly associated with adiposity in mammals and are potential molecular markers for improving meat quality and carcass traits in chickens. In the present study, we screened single nucleotide polymorphisms (SNPs) in all exons of the PLIN1 gene with a direct sequencing method in six populations with different genetic backgrounds (total 240 individuals). We evaluated the association between the polymorphisms and carcass and meat quality traits. We identified three SNPs, located on the 5' flanking region and exon 1 of PLIN1 on chromosome 10 (rs315831750, rs313726543, and rs80724063, respectively). Eight main haplotypes were constructed based on these SNPs. We calculated the allelic and genotypic frequencies, and genetic diversity parameters of the three SNPs. The polymorphism information content (PIC) ranged from 0.2768 to 0.3750, which reflected an intermediate genetic diversity for all chickens. The CC, CT, and TT genotypes influenced the percentage of breast muscle (PBM), percentage of leg muscle (PLM) and percentage of abdominal fat at rs315831750 (p<0.05). Diplotypes (haplotype pairs) affected the percentage of eviscerated weight (PEW) and PBM (p<0.05). Compared with chickens carrying other diplotypes, H3H7 had the greatest PEW and H2H2 had the greatest PBM, and those with diplotype H7H7 had the smallest PEW and PBM. We conclude that PLIN1 gene polymorphisms may affect broiler carcass and breast muscle yields, and diplotypes H3H7 and H2H2 could be positive molecular markers to enhance PEW and PBM in chickens.

• Animal Systematics, Evolution and Diversity
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• 제28권2호
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• pp.133-136
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• 2012

The objective of this study was to determine the degree of mitochondrial DNA (mtDNA) divergence between two subspecies of $Mustela$ $sibirica$ from Korea ($M.$ $s.$ $coreanus$ on the Korean Peninsula and ($M.$ $s.$ $quelpartis$ on Jeju Island) and to examine the taxonomic status of ($M.$ $s.$ $quelpartis$. Thus, we obtained complete sequences of mtDNA cytochrome $b$ gene (1,140 bp) from the two subspecies, and these sequences were compared to a corresponding haplotype of ($M.$ $s.$ $coreanus$, downloaded from GenBank. From this analysis, it was observed that the sequences from monogenic ($M.$ $s.$ $quelpartis$ on Jeju Island were identical to the sequences of four ($M.$ $s.$ $coreanus$from four locations across the Korean Peninsula, and that the two subspecies formed a single clade; the average nucleotide distance between the two subspecies was 0.26% (range, 0.00 to 0.53%). We found that the subspecies $quelpartis$ is not genetically distinct from the subspecies $coreanus$, and that this cytochrome $b$ sequencing result does not support the current classification, distinguishing these two subspecies by pelage color. Further systematic analyses using morphometric characters and other DNA markers are necessary to confirm the taxonomic status of ($M.$ $s.$ $quelpartis$.

• 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 Bioscience
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• 제35권9호
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.