• ANNALS OF ANIMAL RESOURCE SCIENCES
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• v.29 no.4
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• pp.142-149
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• 2018

In this study, 844 Hanwoo proven bulls in South Korea (called KPN) were classified into 8 groups based on their birth year. Microsatellite (MS) marker information for paternity identification of each individual is provided at the homepage of the National Agricultural Cooperation Federation, Korea (NACF) and is mainly for the analysis of genetic diversity and structural changes. The polymorphism analysis of KPN whole groups revealed the average number of alleles in each marker (number of alleles), the expected heterozygosity ($H_{ex}$), the observed heterozygosity ($H_{ob}$), the polymorphism information content (PIC) and the $F_{is}$ mean as 10.54, 0.764, 0.773, 0.727 and -0.014, respectively. For group D, with the birth year 2004-2005, the $H_{ex}$ and $H_{ob}$ were 0.777 and 0.792 respectively and the PIC was 0.740. The $H_{ex}$ of group C and D, with birth years 2003-2004 and 2007-2008, respectively, were greater than $H_{ob}$. In all the other groups, $H_{ob}$ was greater than $H_{ex}$. Genetic composition and structure were analyzed using STRUCTURE software. According to the analyzed results, the generation of Hanwoo groups showed changes in specific genetic components according to the flow. It was confirmed that the continuous improvement in the Hanwoo affects the genetic structure of the proven bulls group. The results of this study are expected to be used for enhancing the efficiency of Hanwoo improvement project.

• Journal of Life Science
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• v.20 no.3
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• pp.336-344
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• 2010

To assess population structure and genetic diversity among the Pacific cod (Gadus macrocephalus), we investigated mtDNA COI gene sequences of 7 populations. Samples were obtained from Sokcho, Wolsung, Geojedo, Yeosu, Geomundo and Westsouth in 2008 and 2009 (n=28). The sequence analysis of 28 individual samples showed 8 haplotypes, ranging in sequence divergence by pairwise comparisons from 0.2 to 2.2% (1 bp-11 bp). The Gal haplotype was found in Wolsung, Geojedo, Yeosu, Geomundo and Westsouth, and was regarded as the main haplotype of Korean Pacific cod. Ga2, Ga3, Ga6 and Ga7 haplotypes were found only in Sokcho. In the PHYLIP analysis, 8 haplotypes formed two independent groups: cladeA consisted of Ga2, Ga3, Ga6 and Ga7 haplotypes, whereas cladeB contained Gal, Ga4, Ga5 and Ga8 haplotypes. The genetic relationship between the two groups was weakly supported by bootstrap analysis(<50%). In pairwise comparisons between 6 populations other than that from Sokcho, a very high per generation migration ratio ($N_m$=infinite) and a very low level of geographic distance ($F_{sr}=-0.0123-(-0.0423)$) were observed. The estimates of genetic distance between Sokcho and the other localities were all statistically significant (p<0.05, p<0.01, p<0.001), indicating a limited mtDNA-based gene flow between Sokcho and other regions. The finding of the lowest genetic diversity in the Sokcho population (nucleotide diversity=0.00589) may be a result of relatively small population size and interrupted gene flow to other localities. Consequently, the overall considerable migration of Pacific cod population in Korea caused a genetically homogeneous structure to form, although a distinct population was found in this study.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.645-652
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• 2007

The origin of domestic donkeys in China has been controversial. To clarify the origin of Chinese domestic donkeys, we investigated the partial mitochondrial D-loop sequences of 126 samples from 12 native breeds. The results revealed two mitochondrial origins, lineage Somali and lineage Nubian of African wild ass detected in Chinese domestic donkeys. Lineage Somali was predominant in Chinese domestic donkey breeds. The pattern of genetic variation in ass mtDNA D-loop sequences indicated that the two lineages Somali and Nubian from China had undergone population expansion events. In a combined analysis of lineages Somali and Nubian between previously published sequences from other countries/regions and sequences of Chinese domestic donkeys, the results indicated that the two lineages of Chinese domestic donkeys were from Africa and supported the African maternal origins of Chinese domestic donkeys. There was no obvious geographical structure in Chinese domestic donkey breeds, but the population showed abundant mtDNA diversity. The spread routes of Chinese domestic donkeys were also discussed.

• Food Science and Biotechnology
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• v.27 no.6
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• pp.1755-1760
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• 2018

The objective of this study was to perform genetic diversity analysis of 13 strains isolated from South Korean foods by multilocus sequence typing (MLST). For typing, seven housekeeping loci (atpA, dnaA, dnaK, gyrB, pheS, pyrG, and rpoA) were selected, amplified and analyzed. Fifty-one polymorphic sites varying from 1 to 22 in each species were identified. Thirteen sequence types were generated with allele numbers ranged from 2 to 10. The overall relationship between strains was assessed by unweighted pair group method with arithmetic mean dendrogram and minimum spanning tree. In addition, combined spits tree analysis revealed intragenic recombination. No clear relationship was observed between the isolation sources and strains. The developed MLST scheme enhanced our knowledge of the population diversity of Leu. citreum strains and will be used further for the selection of industrially important strain.

• Journal of Veterinary Science
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• v.22 no.5
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• pp.73.1-73.11
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• 2021

Background: Feline calicivirus (FCV) is a common pathogen of felids, and FCV vaccination is regularly practiced. The genetic variability and antigenic diversity of FCV hinder the effective control and prevention of infection by vaccination. Improved knowledge of the epidemiological characteristics of FCV should assist in the development of more effective vaccines. Objectives: This study aims to determine the prevalence of FCV in a population of cats with FCV-suspected clinical signs in Hangzhou and to demonstrate the antigenic and genetic relationships between vaccine status and representative isolated FCV strains. Methods: Cats (n = 516) from Hangzhou were investigated between 2018 and 2020. The association between risk factors and FCV infection was assessed. Phylogenetic analyses based on a capsid coding sequence were performed to identify the genetic relationships between strains. In vitro virus neutralization tests were used to assess antibody levels against isolated FCV strains in client-owned cats. Results: The FCV-positive rate of the examined cats was 43.0%. Risk factors significantly associated with FCV infection were vaccination status and oral symptoms. Phylogenetic analysis revealed a radial phylogeny with no evidence of temporal or countrywide clusters. There was a significant difference in the distribution of serum antibody titers between vaccinated and unvaccinated cats. Conclusions: This study revealed a high prevalence and genetic diversity of FCV in Hangzhou. The results indicate that the efficacy of FCV vaccination is unsatisfactory. More comprehensive and refined vaccination protocols are an urgent and unmet need.

• Animal cells and systems
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• v.2 no.2
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• pp.281-285
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• 1998

We examined Y chromosomal DNA polymorphisms at the DYS19 and DXYS5Y loci in a total of 480 unrelated male samples from the Korean population. All five common alleles were identified at the tetranucleotide microsatellite locus DYS19 in this study. The C allele was the most frequent (212/480), followed by D (136/480), B (75/480), E (36/480) and A (21/480) allele. The frequency of Y2 allele at the DXYS5Y locus was found to be 4.6% (22/480). Combining the allelic variation at these two loci resulted in a total of 9 combination haplotypes. The mean combination haplotype diversity wIns 0.72. Based on the results of these two loci, Korean and Japanese populations may share some common genetic structure that is rare or absent in the other ethnic groups. The genetic similarity between Korean and Japanese populations may be due to the large infusion of Y chromosomes through the Yayoi migration starting 2,300 years ago from Korea to Japan.

• Journal of Life Science
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• v.25 no.12
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• pp.1347-1353
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• 2015

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

• Journal of Ecology and Environment
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• v.31 no.2
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• pp.131-137
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• 2008

This study investigated the population densities and diversity of heterotrophic bacteria, and the rhizosphere-to-soil ratios (R/S) in the rhizosphere soil of halophyte Phragmites communis at the western coastal mudflats of Korea. The population densities of aerobic heterotrophic bacteria on the rhizosphere soil of P. communis were in the range of $3.3\;{\pm}\;0.9\;{\times}\;10^7\;{\sim}\;1.2\;{\pm}\;0.5\;{\times}\;10^8\;cfu\;g^{-1}$ dry weight (d. wt.). Population densities of amylolytic bacteria ranged from $1.1\;{\pm}\;0.2\;{\times}\;10^6$ to $3.0\;{\pm}\;1.2\;{\times}\;10^6\;cfu\;g^{-1}\;d.\;wt.$, while those of cellulolytic bacteria and proteolytic bacteria ranged from $5.6\;{\pm}\;2.3\;{\times}\;10^6$ to $1.5\;{\pm}\;0.3\;{\times}\;10^7\;cfu\;g^{-1}\;d.\;wt.$ and from $1.4\;{\pm}\;0.3\;{\times}\;10^6$ to $3.5\;{\pm}\;2.3\;{\times}\;10^7 \;cfu\;g^{-1}\;d.\;wt.$, respectively. The R/S ratios ranged from 2.26 to 6.89. Genetic (16S DNA) analysis of fifty-one isolates from the roots of P. communis suggested that the dominant species were closely related to the ${\gamma}$-proteobacteria group (18 clones) and the ${\alpha}$-proteobacteria group (14 clones). We found that halophyte species and mudflat environment both affected the rhizosphere bacterial communities.

• Journal of Korean Society of Forest Science
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• v.90 no.2
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• pp.169-175
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• 2001

Genomic DNAs were extracted from the leaves of 182 ginkgo trees (Ginkgo biloba L.) planted in 6 regions and subjected to the analysis of both I-SSR and RAPD markers. A total of 227 amplicon variants were generated by PCR using 15 I-SSR primers and 67 amplicons by PCR with 5 RAPD primers. Levels of genetic diversity within 6 populations were turned out to be similar (Shannon's Index, I-SSR : 0.35~0.40; mean of 0.38, RAPD : 0.31~0.38; mean of 0.35, combined : 0.35~0.40; mean of 0.37). Ranks of the level of genetic diversity estimated from I-SSR, RAPD, and combined data were not coincided each other. Majority of genetic diversity was allocated among individuals within populations (I-SSR : 94.31%, RAPD : 93.62%, combined : 93.57%), which resulted in pretty low level of population differentiation. Genetic differentiation between male and female groups was turned out to be quite low (I-SSR : 0.03, RAPD : 0.091, combined : 0.043), which slightly fluctuated when analysis was restricted to the data obtained from 3 regions where both male and female trees were sampled (I-SSR : 0.038, RAPD : 0.084, combined : 0.047). Genetic relationships among the populations, reconstructed by UPGMA, were not coincided with geographic affinity, which might be resulted from sharing of seed sources in some regions. Whereas independent cluster analyses with I-SSR data and RAPD data, respectively, reclassified by sexes revealed two sexual groups in which all the male and the female populations were clustered together, cluster analysis with combined data did not show clear sexual grouping.

• Journal of Life Science
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• v.25 no.11
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• pp.1204-1213
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• 2015

A comprehensive analysis of the population structure of the sandfish (Arctoscopus japonicas), the most abundant fishery resource in the East Sea of Korea, has not been carried out, despite its importance in Korea. The present study examined the genetic diversity and differences between five populations (two Japanese and three Korean populations) of A. japonicas captured in the East Sea using both the 401 bp sequence of mitochondrial DNA (mtDNA, cytochrome b) and five microsatellite DNA (msDNA) markers. The results of the analysis using the Cyt b sequence revealed 27 haplotypes. Based on msDNA variations, the estimated expected heterozygosity (H_E) in each population ranged from 0.68 (Gampo, Korea) to 0.7765 (Erimo, Japan). Pairwise F_ST and AMOVA tests using both the Cyt b sequence and msDNA data pointed to significant differences between the Korean and Japanese populations (mtDNA; F_ST=0.2648, p<0.05, msDNA; F_ST=0.0814, p<0.05). These results were similar to the results of UPGMA, PCA, and structure analysis. In these analyses, the five populations were assigned to two groups (Korean populations and Japanese populations). These results shed light on the genetic diversity and relationships of A. japonicas and contribute to research on the evaluation, conservation, and utilization of Korean A. japonicas as genetic resources.