• BMB Reports
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• v.46 no.8
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• pp.416-421
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• 2013

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

• Fisheries and Aquatic Sciences
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• v.14 no.4
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• pp.295-301
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• 2011

We investigated the genetic structure of Korean and Japanese ayu Plecoglossus altivelis populations by examining 669 individuals from 14 populations using three microsatellite loci. Genetic variation did not differ significantly among the populations examined in terms of allelic number and heterozygosity. Korean populations were genetically close to each other, implying that persistent gene flow has occurred in these populations. This suggests that eastern populations in Korea form a single large population and all of the Korean populations are distinct from the Japanese populations. Pairwise population $F_{ST}$ estimates, principal component analyses, and a neighbor-joining tree showed that genetic separation between the southern and pooled eastern coast populations was probably influenced by restricted gene flow. Hierarchical analysis of molecular variance (AMOVA) revealed a weak but significant genetic structure among three ayu groups (eastern and southern coasts of Korea and the Japan coast), and no genetic variation within groups. The estimated genetic population structure and potential applications of microsatellite markers may aid in the proper management of ayu populations.

• Animal Systematics, Evolution and Diversity
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• v.32 no.2
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• pp.105-111
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• 2016

The genetic structure of marine animals that inhabit the seashore is affected by numerous factors. Of these, gene flow and natural selection during recruitment have strong influences on the genetic structure of seashore-dwelling species that have larval periods. Relative contributions of these two factors to the genetic structure of marine species would be determined mainly by the duration of larval stage. The relationship between larval period and genetic structure of population has been rarely studied in Korea. In this study, genetic variations of cytochrome oxidase subunit I (COI) were analyzed in two dominant species on rocky shore habitats in the Korean peninsula: periwinkle Littorina brevicula and acorn barnacle Fistulobalanus albicostatus. Both species are not strongly structured and may have experienced recent population expansion. Unlike periwinkle, however, barnacle populations have considerable genetic variation, and show a bimodal pattern of mismatch distribution. These results suggest that barnacle populations are more affected by local adaptation rather than gene flow via larval migration. The bimodal patterns of barnacle populations observed in mismatch distribution plots imply that they may have experienced secondary contact. Further studies on seashore-dwelling species are expected to be useful in understanding the evolution of the coastal ecosystem around Korean waters.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.04a
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• pp.32-32
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• 2019

Mutation breeding is the useful tool to improve agronomic traits in various crop species. Soybean is most important crop and is rich in protein and oil contents. Despite of the importance as economic value and various genetic resource of soybean, there have been limited studies of genetic relationship among mutant resources through radiation breeding. In this study, the agronomical phenotype for selecting various genetic resources was evaluated in 528 soybean mutant lines. As a result, 210 soybean mutants with their original cultivars were selected with various traits. We named 210 selected lines as Mutant Diversity Pool (MDP). The genetic diversity and the relationship of the MDP were investigated using TRAP and TE-TRAP markers. In TRAP analysis, sixteen primer combination (PC)s were used and a total of 551 fragments were amplified. The highest (84.00%) and the lowest (32.35%) polymorphism levels were showed in PC MIR157B+Ga5 and B14G14B+Ga3, respectively. The mean of PIC values was 0.15 ranging from 0.07 in B14G14B+Sa12 to 0.23 in MIR157B+Sa4. Phylogenetic and population structure analysis indicated that the 210 MDP lines dispersed to four groups among the wild types and their mutants. The highest genetic diversity among populations was observed between lines Paldal and 523-7 (Fst=0.409), whereas the lowest genetic diversity was between population KAS360-22 and 94seori (Fst=0.065). AMOVA showed 11.583 (21.0%) and 43.532 (79.0%) variations in inter and intra mutant population, respectively. Overall, the genetic similarity of each intra mutant populations was closer than that of inter mutant population. A total of 408 fragments were amplified in the 210 MDP using twelve PCs of TE-TRAP markers that were obtained from a combination of three TIR sequence of transposable elements (MITE-stowaway; M-s, MITE-tourist; M-t, PONG). The highest (77.42%) and the lowest (56.00%) polymorphism levels were showed in PONG+Sa4 and PONG+Sa12, respectively. The mean of PIC values was 0.15 ranging from 0.09 in M-s+Sa4 and M-s+Ga5 to 0.21 in M-t+Ga5. AMOVA of M-s showed 2.209 (20%) and 8.957 (80%) variations in inter and intra mutant population, respectively. AMOVA of M-t showed 2.766 (18%) and 12.385 (82%) variations in inter and intra mutant population, respectively. AMOVA of PONG showed 3.151 (29%) and 7.646 (71%) variations in inter and intra mutant population, respectively. According to our study, the PONG had higher inter mutant population and lower intra mutant population. This mean was that for aspect of radiation sensitivity, M-s and M-t showed higher mobility than that of PONG. Our results suggest that the TRAP and the TE-TRAP markers may be useful for assessing the genetic diversity and relationship among soybean MDP and help to improve our knowledge of soybean mutation/radiation breeding.

• Korean Journal of Plant Taxonomy
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• v.47 no.1
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• pp.1-5
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• 2017

The population status of Hydrangea luteovenosa Koidz. in Korea was investigated, with an emphasis on its genetic diversity. From field surveys, we obtained the only locality record for a wild population in Jeju Island, which contained 285 individuals in total. Genotyping was performed using five microsatellite markers for the all extant plants in Korea. Three Japanese populations were also genotyped for the comparative analyses. The genotyping result showed that the Jeju population consisted of only two multilocus genotypes, including identical heterozygous genotypes at two loci; it had been maintained mostly by vegetative reproduction; and although the Jeju population is geographically far from Japanese populations, all alleles observed in the Korean population were shared with Japanese populations, suggesting the possibility that H. luteovenosa in the Jeju Island had been recently migrated or introduced from Japan. Future ecological and genetic studies associated with negative effects of low genetic variation will be essential for determining the conservation direction of the threatened Korean population of this species.

• Journal of Life Science
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• v.16 no.6
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• pp.898-903
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• 2006

The genetic diversity and population structure of fifteen Potentilla discolor Bunge populations in Korea were determined using genetic variations at 19 allozyme loci. Fourteen of the 19 loci (73.7%) showed detectable polymorphism. Genetic diversity at the species level and at the population level was high ($H_{ES}\;=\;0.215$, $H_{EP}\;=\;0.196$, respectively), whereas the extent of the population divergence was relatively low $(G_{ST}\;=\;0.069)$. Total genetic diversity values $(H_T)$ varied between 0.0 and 0.656, giving an average overall polymorphic loci of 0.292. The interlocus variation of genetic diversity within populations $(H_S)$ was high (0.274). On a per locus basis, the proportion of total genetic variation due to differences among populations $(G_{ST})$ ranged from 0.010 for Pgm-2 to 0.261 for Pgd-2 with a mean of 0.069, indicating that about 6.9% of the total allozyme variation was among populations. Wide geographic ranges, perennial herbaceous nature and the persistence of multiple generations are associated with the high level of genetic variation in P. discolor. The estimate of gene flow based on $G_{ST}$ was high among Korean populations of P. discolor (Nm = 3.36).

• International Journal of Industrial Entomology and Biomaterials
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• v.24 no.1
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• pp.41-47
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• 2012

The Scarites aterrimus (Coleoptera: Carabidae) dwells exclusively on coastal sandy dunes. Previously, we investigated the nation-wide magnitude and nature of genetic diversity of the species using mitochondrial COI gene and found moderate to low magnitude of sequence diversity, the presence of closely related haplotypes, and relatively high gene flow estimate. Based on these observations we concluded that the species had no historical barriers that bolster genetic subdivision and possible population decline. In this study, we additionally sequenced mitochondrial COII gene from 23 individuals collected from 9 Korean localities to confirm previous findings. Sequencing of 688 bp COII gene provided 5 haplotypes ranging in sequence divergence from 0.145% to 0.291% (1 ~ 2 bp), further confirming low sequence divergence of the species. Gene flow estimates and genetic diversity estimates also support the previous findings that there had been no historical barriers that bolster genetic subdivision.

• Animal cells and systems
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• v.8 no.4
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• pp.289-294
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• 2004

Bupleurum latissimum is a narrowly endemic and endangered plant, restricted to only two small populations on steep cliffs of a small island, Ulleung Island, in Korea. The genetic diversity and population differentiation in the two remnant populations of the species were investigated using RAPD (random amplified polymorphic DNA) analysis. The Neis gene diversities were 0.146 in the smaller population of 45 individuals, and 0.151 in the larger population of 61 individuals. The genetic variation was not significantly different between these two populations. Genetic diversity within populations was not low considering the very small size of populations. Analysis of molecular variance (AMOVA) revealed higher variation within populations (65.9%) than genetic differentiation between them (34.1%). B. latissimum revealed higher population differentiation than other outbreeding species. The differentiation of the populations corresponded to low gene flow (Nem = 0.482). The cluster and principal coordination analyses provide strong support for high population differentiation, showing that all individuals of the two populations have built up population-specific clusters. Although gene flow between the two populations of B. latissimum was limited, they have preserved relatively high levels of genetic variation.

• International Journal of Industrial Entomology and Biomaterials
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• v.22 no.2
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• pp.65-74
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• 2011

The Scarites aterrimus (Coleoptera: Carabidae), is one of the carabid beetles dwelling exclusively on coastal sandy dunes. Habitat deterioration and equivalent activity have greatly concerned population declines in several species dwelling on the coastal sandy dunes. As a first step to establish long-term conservation strategy, we investigated the nation-wide magnitude and nature of genetic diversity of the species. As a first step, we sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region (658 bp) from a total of 24 S. aterrimus individuals collected over nine sandy dunes belonging to four Korean provinces. The sequence analysis evidenced moderate to low magnitude of sequence diversity compared with other insect species distributed in Korean peninsula (0.152% to 0.912%). The presence of closely related haplotypes and relatively high gene flow estimate collectively suggest that there had been no historical barriers that bolster genetic subdivision. Population decline was postulated on the basis of several missing haplotypes that are well found in the species with a large population size. This interpretation is consistent with field observation of small population size in the coastal sandy dune habitats. The highest genetic diversity estimates were found in the coastal sand dune population of Seogwipo, Jeju Island, justifying a prior attention to the population, in order to sustain overall genetic diversity of the species. Further scrutinized study might be required for further robust conclusion.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.3 no.4
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• pp.191-198
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• 2022

Natural habitats of the Korean long-tailed goral (Naemorhedus caudatus) have been fragmented by anthropogenic activities in South Korea in the last decades. Here, the individual identity, genetic variation, and population differentiation of the endangered species were examined via the multiple-tube approach using a non-invasive genotyping method. The average number of alleles was 3.16 alleles/locus for the total population. The Yanggu population (1.66) showed relatively lower average number of alleles than the Inje population (3.67). Of the total 19 alleles, only seven (36.8%) alleles were shared by the two populations. Using five polymorphic out of six loci, four and six different goral individuals from the captive Yanggu (n=24) and the wild Inje (n=28) population were identified, respectively. The allele distribution was not identical between the two populations (Fisher's exact test: P<0.01). A considerably low migration rate was detected between the two populations (no. of migrants after correction for size=0.294). Additionally, the F statistics results indicated significant population differentiation between them, however, quite low (F_ST=0.327, P<0.01). The posterior probabilities indicated that the two populations originated from a single panmictic population (P=0.959) and the assignment test results designated all individuals to both populations with nearly equal likelihood. These could be resulted from moderate population differentiation between the populations. No significant evidence supported recent population bottleneck in the total Korean goral population. This study could provide us with useful population genetic information for conservation and management of the endangered species.