• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Journal of Life Science
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• v.22 no.4
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• pp.466-471
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• 2012

Sixty individuals of the scallop $Patinopecten$ $yessoensis$ (Genus Pecten) were sampled to examine the genetic diversity and population structure of this species. Random amplified polymorphic DNA (RAPD) identified 109 genotypes and produced 79 polymorphic loci (72.8%). Total genetic diversity values ($H_T$) and interlocus variation in the within-population genetic diversity ($H_S$) were 0.254 and 0.178, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) was 0.299. This indicated that about 70.1% of the total variation was within populations. The unique loci and bands of $P.$ $yessoensis$ were shown in only one population among the three countries. RAPD markers were very effective in classifying the natural population levels of $P.$ $yessoensis$ in Korea, China, and Japan. In addition, insights into the relative gene diversity among and within populations of $P.$ $yessoensis$ would be useful in breeding and for the development of strategies for animal genetic resources.

• Journal of Life Science
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• v.20 no.10
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• pp.1538-1543
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• 2010

This study was conducted to examine the genetic diversity and population structure of 17 Brassica juncea populations in Korea. The technique of random amplified polymorphic DNA (RAPD) produced 60 polymorphic loci and 18 monomorphic loci. In a simple measure of intraspecies variability by the percentage of polymorphic bands, the Jindo population of Cheonnam showed the highest (29.5%). The cultivar exhibited the lowest variation (12.8%). Mean number of alleles per locus (A) and the effective number of alleles per locus ($A_E$) were 1.221 and 1.167, respectively. As the typical populations of this species were small, isolated, and patchily distributed in their natural populations, they maintained a low level of genetic diversity of fourteen primers. On a per locus basis, total genetic diversity values ($H_T$) and interlocus variation in the within-population genetic diversity ($H_S$) were 0.347 and 0.141, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) was 0.589. This indicated that about 58.9% of the total variation was among populations. The estimate of gene flow, based on $G_{ST}$, was very low among Korean populations of B. juncea ($N_m$=0.617). These results suggest that the geological distance dispersal of wild B. juncea is the best event. RAPD markers are very effective in classifying natural population levels of B. juncea in Korea.

• Animal Systematics, Evolution and Diversity
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• v.39 no.4
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• pp.264-271
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• 2023

The edible jellyfish Rhopilema esculentum occurs in waters throughout northeastern Asia, including in Korea, China, and Japan. In Korean waters, R. esculentum has appeared in two regions (Gangwha and Muan). Based on the appearance of young medusae and coastal distribution records, these two regions may be key R. esculentum breeding sites. In the present study, we investigate and compare the genetic structure of R. esculentum in the two regions using mitochondrial sequences (16S ribosomal RNA and cytochrome c oxidase subunit I). The genetic diversity of the R. esculentum population at Ganghwa exceeded that of the population at Muan. Despite considerable geographic separation (400 km) between the two regions(Gangwha and Muan), our haplotype network suggests that the Gangwha and Muan populations of R. esculentum are related. The simple and monotonous genetic structure of the Muan population shows that R. esculentum emergence is relatively recent. In contrast, the Gangwha population shows evolution. Moreover, jellyfish of the Gangwha population are genetically diverse and remain constant despite environmental fluctuations in the Han River. The Gangwha area is considered to be the old origin of R. esculentum in Korea.

• ALGAE
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• v.36 no.1
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• pp.13-24
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• 2021

The present-day genetic structure of macroalgal species reflects both geographical history and oceanic circulation patterns as well as anthropogenic introduction across native ranges. To precisely understand the genetic diversity and how the factors shape the current population structure of Gloiopeltis furcata sensu lato, we determined the mitochondrial 5' end of cytochrome c oxidase subunit I (COI-5P) sequences for 677 individuals sampled from 67 sites spanning almost the entire distribution range in Korea and Japan. Results from the phylogenetic analysis and haplotype distribution revealed eleven distinct lineages within G. furcata s.l. along the Korea-Japan coastal areas and displayed divergent phylogeographic patterns among lineages. Despite the closely related lineages distributed in same habitats as high rocky intertidal zone, they display different phylogeographic patterns among lineages. The populations from the south of Korea-Japan harbored the highest genetic diversity and unique endemism in comparison with other populations in the distribution range. This could be the evidence of southern refugia for G. furcata s.l. in the Northwest (NW) Pacific and the recent migration from native to introduced region. The reason is that an exceptional distribution pattern was found high genetic diversity in Hakodate of Japan where is the northern location in the NW Pacific. Our results imply the contemporary influence on the distribution due to current circulation pattern and anthropogenic effects. These phylogeographic findings provide the important insight into cryptic species diversity and the detailed distribution pattern of Gloiopeltis in the NW Pacific.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.220-220
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• 2022

Disproportionating Enzyme 1 (DPE1) is an a-1,4-D-glucanotransferase that cleavages the a-1,4-glucosidic bonds and transfers glucosyl groups. In rice endosperm, it participates in starch synthesis by transferring maltooligosyl groups from amylose and amylopectin to amylopectin. Here, we investigated the haplotype variations and evolutionary indices (e.g., genetic diversity and population structure) for the DPE1 gene in 374 rice accessions representing seven subgroups (wild, indica, temperate japonica, tropical japonica, aus, aromatic, and admixture). Variant calling analysis of DPE1 coding regions leads to the identification of six functional haplotypes representing/occupying 8 nonsynonymous SNPs. Nucleotide diversity analysis revealed the highest pi-value in wild group (0.0556) compared to other cultivated groups, of which temperate japonica showed the most reduction of genetic diversity value (0.003). A significant positive Tajima's D value (1.6330) of admixture highlights sudden population contraction under balancing selection, while temperate japonica with the lowest Tajima's D value (-1.3523) showed a selection signature of DPE1 domestication which might be the cause of excess of rare alleles. Moreover, these two subpopulations exhibits a greater differentiation (F_ST=0.0148), indicating a higher genetic diversity. Our findings on functional DPE1 haplotypes will be useful in future breeding programs, and the evolutionary indices can also be applicable in functional studies of the DPE1 gene.

• Journal of Forest and Environmental Science
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• v.24 no.1
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• pp.27-34
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• 2008

Level and distribution of genetic diversity in seven populations of Albizia lucida Benth. in eastern region of the Indian sub-continent were estimated using ISSR markers. Relatively higher level of genetic diversity within populations was observed in seven populations of A. lucida (mean of 0.38). From the result of AMOVA, majority of genetic diversity was allocated within populations (96.2%) resulting in a moderate degree of population differentiation. The observed distribution pattern of I-SSR variant among the populations was coincided with the typical pattern of long-lived woody tree species. Genetic relationships among the populations, reconstructed by UPGMA method, revealed two genetic groups. The population of Anugul and Bargarh turned out to be the most closely related despite a distance location between them. These formations will be of great value in the development of conservation plans for species exhibiting high levels of genetic differentiation due to fragmentation, such as indication of conservation unit size, which populations should be chosen as priority in conservation plans and which samples should be introduced in areas with a low number of individuals of A. lucida.

• Journal of Life Science
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• v.8 no.6
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• pp.687-694
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• 1998

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Chimaphila japonica Miq. in Korea. The percent of polymorphic loci within the enzymes was 48.7%. Genetic diversity at the species level and at the population level was high (Hes=0.278 ; Hep=0.222, respectively), whereas the extent of the population divergence was relatively low ( $G_{ST}$ =0.079). $F_{IS}$ , a measure of the deviation from random mating within the 7 populations, was 0.355. An indirect estimate of the number of migrants per generation (Nm=2.61) indicates that gene flow is high among Korean populations of the species. In addition, analysis of fixation indices revealed a substantial heterozygosity deficiency in some populations and at some loci. Factors contributing to the high levels of genetic dive-rsity found in the entire species of C. japonica include wide distribution, long-lived perennials, ability to regenerate due to rhizomatous spread, outcrossing induced by animal vectors, and occasional pollen dispersal by wind.

• Journal of Korean Society of Forest Science
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• v.95 no.4
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• pp.435-442
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• 2006

A total of 167 peculiar haplotypes confirmed from 28 cpSR variants that were observed in 19 populations of Japanese red pine in Korea through cpSSR marker analysis. Thirteen individuals that showed identical haplotype dispersed evenly in 10 populations, and the average number of effective haplotype within population was 13.37. Estimate of genetic diversity (He) was 0.987 on the basis of cpSSR haplotype variants that was equivalent to or higher than the estimates reported in other studies on some forest tree species. Estimation of genetic diversity (S.I.) on the basis of cpSSR variants composing each haplotype revealed the highest estimate of 1.109 for the population of Gangwon-Yeongwol and the lowest estimate of 0.411 for the population of Gyeongbuk Mungyeong with the average of 0.887. Most of observed cpSSR variants appeared to exist commonly in 19 populations (97.62%), and genetic differentiation of cpSSR variants among populations was turned out to be weak (${\Phi}_{ST}=0.024$). Relatively fast rate of mutation of cpSSR marker might be a major cause for such weak population differentiation. There was no identical haplotype shared between 39 population pairs of 173 pair-wise population pairs. Estimation of genetic distance among 19 populations on the basis of population pairs was also impossible, that might be resulted from restricted migration among 19 populations. Considering the observed distribution patterns of cpSSR variants in addition to the previous studies on I-SSR variants, informations on the present geographic location and genetic status of populations should be considered together for effective sustainable management of the genetic resources of Japanese red pine in Korea.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.660-670
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• 2014

The Korean plum yew (Cephalotaxus koreana Nakai) is a shade-tolerant, coniferous shrub. The seeds have been used as a folk medicine in Korea, and an alkaloid extract (HTT) is known to have anticancer properties. We estimated the genetic diversity of 429 trees in 16 populations in South Korea using 194 polymorphic amplicons from seven combinations of AFLP primer-restriction enzymes. The average number of effective alleles and the percentage of polymorphic loci were 1.37 and 79.4%, respectively. Shannon's diversity index and the expected heterozygosity were 0.344 and 0.244, respectively. We divided 16 populations into four groups on the UPGMA dendrogram and the PCA biplot. The first two principal components explained 84% of the total genetic variation. Genetic differentiation between populations explained 14% of total genetic variation, and the remaining 86% came from difference between individuals within populations, as determined by an analysis of molecular variance (AMOVA). However, the genetic differentiation did not correlate with the geographic distance between populations from the Mantel test. The Bayesian statistics, which are comparable to Wright's $F_{ST}$ and Nei's $G_{ST}$, were ${\theta}^I=0.406$ and ${\theta}^{II}=0.172$, respectively. The population genetic diversity was slightly lower, and the strength of genetic differentiation was much weaker, than the average of those plants having similar life histories, as assessed using arbitrary marker systems. We discuss strategies for the genetic conservation of the plum yew in Korea.