• Journal of Life Science
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• v.30 no.3
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• pp.291-297
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• 2020

This study was conducted to develop microsatellite markers in Seriola quinqueradiata using next-generation sequencing. A total of 28,873,374 reads were generated on an Illumina Hiseq2500 system, yielding 7,247,216,874 bp sequences. The de novo assembly resulted in 466,359 contigs. A total of 132 contigs (0.43%), including 60 microsatellite loci, were derived from 30,729 contigs longer than 518 bp. A total of 60 primer sets were designed from the 132 microsatellite loci. A total of 15 polymorphic nuclear microsatellite loci were chosen to evaluate population genetic parameters in the parents and offspring. The mean number of effective alleles was 18.5, ranging from 11 to 30. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged between 0.431 and 0.972 with an average of 0.812 and from 0.782 to 0.949 with an average of 0.896, respectively. No significant linkage disequilibrium was observed after Bonferroni revision in any loci. The results show that the 15 polymorphic nuclear microsatellite markers can be used to study the population and conservation genetics of S. quinqueradiata in Korea. To ensure the success of artificial seedling production technology, genetic variations between the parent and offspring populations should be monitored, and inbreeding should be controlled.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.11
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• pp.102-108
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• 2020

This study was conducted to investigate the genetic diversity and genetic taxonomic relationships between Korean native black goat (KNBG) populations and crossbred goats. The 45,658 common single nucleotide polymorphisms present in the KNBG strain and crossbred goat were used for the analysis. The expected and observed heterozygosity (which can be indicators of genetic diversity) were in the order of crossbred, Gyeongsang National University, Jangsu, then the Tongyeong strains. The variance component represents the degree of genetic diversity between groups. The highest variance (19.98 %) was between the Dangjin and Gyeongsang National University strains. The lowest variance (8.87 %) was between the Jangsu and Tongyeong strains. In addition, the genetic distance between the populations showed that Jangsu and Tongyeong formed one branch (they were very similar genetically). The Dangjin and the Gyeongsang National University strains appeared to form a second branch. Furthermore, the crossbred formed one branch with the Dangjin and the Gyeongsang National University strains. Therefore, the results of this study can be used as basic data to reduce unnecessary inbreeding and genetic resource flow between the KNBG populations. The basic data indicates the uniqueness of the genetic resources of the domestic lineage. These findings provide a basis for differentiating KNBG and Crossbred goats to use to improve the desirable characteristics of this species.

• Journal of Korean Society of Forest Science
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• v.103 no.2
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• pp.182-188
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• 2014

Genetic diversity and genetic differentiation in six natural populations of Abies holophylla Max were investigated using ISSR marker system. From 6 ISSR primers, the average percentage of polymorphic loci was 85.6%, and the average expected heterozygosity ($H_e$) was 0.288. From the result of AMOVA, 94.4% of total genetic variation came from the differences among individuals within populations, and 5.6% was caused by those of among-populations. On the basis of Bayesian inference, genetic differentiation (${\theta}^{II}$ and $G_{ST}$) and inbreeding coefficient for all populations were 0.045, 0.038, and 0.509, respectively. The correlation between genetic distance and geographical distance was highly significant at the Mental's test (r = 0.74, P < 0.05). Six populations divided into two groups according to the results of UPGMA and PCA. One group included Namwon, Cheongdo and Mungyeong population. The other was Inje, Hongcheon and Pyeongchang population. Also, in Bayesian clustering analysis, 6 populations were divided into two clusters. But Cheongdo population was assigned into the other cluster unlike those of UPGMA or PCA. Taking the regions based on the results of the cluster analysis into consideration of AMOVA, 3.9% of genetic variation came from the regional difference. The dendrogram from UPGMA could provide the most genetically reasonable explanation for the distribution of Abies holophylla populations in South Korea.

• Journal of Animal Science and Technology
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• v.44 no.4
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• pp.383-390
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• 2002

The data were consisted of 1,262 records for carcass traits observed at Hanwoo steers from 1998 to 2001 at Namwon and Deakwanryung branch of National Livestock Research Institute, Rural Development Administration. Pedigrees of young bulls were traced back to search for magnifying inbreeding. Genetic parameters for carcass traits with Gibbs sampling in a threshold animal model were compared to estimates with REML algorithm in linear model. As the results, most of bulls were not inbred and sire pedigree group was non-inbred population. However, most of the bulls fell in some relationship with each other. Heritability estimates as fully posterior means by Gibbs samplers in threshold model were higher than those by REML in linear model. Furthermore, these estimates in threshold model using GS showed higher estimates than estimates using tested young bulls in previous study and same model. Heritability estimate by GS for marbling score was 0.74 and genetic correlation estimate between marbling score and body weight at slaughter was –0.44. Further study for correlation of breeding values between REML algorithm in linear model and Gibbs sampling algorithm in threshold model was needed.

• Journal of Ginseng Research
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• v.33 no.3
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• pp.199-205
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• 2009

Ginseng (Panax ginseng C.A. Meyer) is one of the most important medicinal plants in East Asia. Microsatellite or simple sequence repeat (SSR) markers are used in obtaining genetic analysis and authentication in many plants. The present study examined five microsatellites in conjunction with P. ginseng in Korea. The total observed allelic number was 17 (mean = 3.4), and gene diversities varied from 0.078 to 0.543 with an average of 0.314. Through a combined analysis of five loci in 100 ginseng samples, 44 different combined genotypes were observed. Expected and observed heterozygosites ranged from 0.077 to 0.541 (mean = 0.313) and 0.040 to 0.130 (0.083), respectively. All examined loci exhibited deficiency of heterozygosity and deviation from the Hardy-Weinberg equilibrium. Such results may be explained by the non-random mating and inbreeding that has occurred for several hundred years. These microsatellite markers could be used for the study of molecular genetics and the establishment of DNA marker database, as well as authentication of ginseng species and chromosomal mapping of QTL loci in P. ginseng.

• Development and Reproduction
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• v.5 no.2
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• pp.151-158
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• 2001

Genomic DNA from the blood of crucian carp(Carassius carassiu) from lake and aquaculture facility in Kunsan, Korea was extracted in order to identify genetic differences by polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD). Out of 12 primers, 6 generated 266 highly reproducible RAPD markers, producing approximately 2.1 polymorphic bands per primer in crucian carp from lake. The degree of similarity varied from 0.18 to 0.76 as calculated by bandsharing analysis in crucian carp from lake. The RAPD outlines obtained with DNA of two different crucian carp populations from Kunsan were different(0.47 from lake and 0.70 from aquaculture facility, respectively). The electrophoretic analysis of polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD) products showed high levels of similarity between different individuals in crucian carp from aquaculture facility. This result implies the genetic similarity due to raising in the same environmental condition or inbreeding within the crucian carp from aquaculture facility in Kunsan. In other words, crucian carp may have high levels of genome DNA diversity due to the introduction of the wild population from the other sites of Knsan even if it may be the geographical diverse distribution of this species. Generally, the RAPD polymorphism generated by these primers may be useful as a genetic marker for strain or population identification of important aquacultural fish species, crucian carp. However, in future, additional populations and sampling sites will be necessary to complement weak points.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.11
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• pp.1691-1699
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• 2018

Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.272-280
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• 2016

Chrysanthemum is one of the top floriculture species with ornamental and medicinal value. Although chrysanthemum breeding program has contributed to the development of various cultivars so far, it needs to be advanced from the traditional phenotype-based selection to marker-assisted selection (molecular breeding) as shown in major cereal and vegetable crops. Molecular breeding relies on trait-linked molecular markers identified from genetic, molecular, and genomic studies. However, these studies in chrysanthemum are significantly hampered by the reproductive, genetic, and genomic properties of chrysanthemum such as self-incompatibility, inbreeding depression, allohexaploid, heterozygosity, and gigantic genome size. Nevertheless, several genetic studies have constructed genetic linkage maps and identified molecular markers linked to important traits of flower, leaf, and plant architecture. With progress in sequencing technology, chrysanthemum transcriptome has been sequenced to construct reference gene set and identify genes responsible for developments or induced by biotic or abiotic stresses. Recently, a genome sequencing project has been launched on a diploid wild Chrysanthemum species. The massive sequencing information would serve as fundamental resources for molecular breeding of chrysanthemum. In this review, we summarized the current status of molecular genetics and genomics in chrysanthemum and briefly discussed future prospects.

• Journal of Korean Society of Forest Science
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• v.102 no.1
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• pp.122-128
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• 2013

Genetic diversity and population genetic structure were estimated in nine natural populations of Exochorda serratifolia in South Korea using ISSR marker system. Average of polymorphic loci per primer was 5.8 (S.D.=2.32) and percentage of polymorphic loci per population was 78.7% with total 35 loci from 6 ISSR primers. In AMOVA, 27.8% of total genetic variation came from genetic difference among populations and 72.2% was resulted from difference among individual trees within populations. Genetic differentiations by Bayesian inference were 0.249 of ${\theta}^{11}$ and 0.227 of $G_{ST}$. Inbreeding coefficient for total populations was 0.412. There was significant correlation between genetic distance and geographic distance among populations. On the results of Bayesian cluster analysis, nine populations were assigned into three groups. The first group included 5 populations, and the second and the third had two populations per group, respectively. These three regions could explain 10.0% of total genetic variation from hierarchical AMOVA, and the levels of among-population and among-individual were explained 19.7% and 70.3%, respectively. The geographic distribution of populations following the three Bayesian clusters could be explained with mountain range as Baekdudaegan which is the main chain of mountains in Korea. The mountains as the physical barrier might hamper gene flow in the pearlbush. So when protected areas are designated for conservation of this species, we should consider those three regions into considerations and would better to choose at least one population per region.

• Journal of Aquaculture
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• v.19 no.3
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• pp.205-209
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• 2006

Genetic change from broodstock to hatchery stock of the olive flounder Paralichthys olivaceus and effective number of breeders (Ne) were investigated by the different fertilized-egg collecting methods; E1 (eggs collected one day after spawning) and E2 (eggs collected two days after spawning) using seven microsatellite loci (Kop2, Kop22, Kop18, Kop3, Kop21, Kop9 and Kop26) for the better understanding of stock enhancement. Observed heterozygosity in three stocks ranged from 0.651 at Kop3 to 0.928 at Kop22, with offspring being slightly higher heterozygous over their parents. However, the genetic reduction of offspring was significant. The offspring allele number per locus was reduced to 23.5% for E1 and 17.6% for E2 of their maternal number. Ne to the hatchery stock was estimated to be 21.9 for E1 and 34.3 for E2. The inbreeding coefficients of populations El and E2 were 0.023 and 0.015, respectively. The present study suggests the extension of the egg collection period for a recovery of the genetic diversity in artificially produced offspring.