• 한국작물학회지
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• 제65권4호
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• pp.447-456
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• 2020

Peanut is an allotetraploid derived from a single recent polyploidization. Polyploidization has been reported to have caused significant loss in genetic diversity during the domestication of cultivated peanuts. Single nucleotide polymorphism (SNP)-based markers such as cleaved amplified polymorphic sequences (CAPS) derived from next-generation sequencing (NGS) have been developed and widely applied for breeding and genetic research in peanuts. This study aimed to identify the genetic diversity and population structure using 30 CAPS markers and 96 peanut accessions from five different origins. High genetic dissimilarities were detected between the accessions from Korea and those from the other three South American origins generally regarded as the origin of peanuts, while the accessions from Brazil and Argentina presented the lowest genetic dissimilarity. Based on the results of the present study, accessions from Korea have unique genetic variation compared to those from other countries, while accessions from the other four origins are closely related. Our study identified the genetic differentiation in 96 peanut accessions from five different origins, and this study also showed the successful application of SNP information derived from re-sequencing based on NGS technology.

• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2001년도 후기 제12차 학술대회 논문집
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• pp.34-35
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• 2001

RAPD analysis based on numerous markers have been used to investigate patterns of genetic differentiation ann and within two cultured and wild populations represented by the species crucian carp(Carassius carassius). From RAPD analysis using five primers, a total of 442 polymorphic bands were obtained in two populations and 273 were found to be specific to a wild population. According to RAPD-based estimates, average number of polymorphic bands in wild population was approximately 1.5 times as diverse as that in cultured. The average level of bandsharing values was $0.40 \pm 0.05$ in wild population, but was $0.69 \pm 0.08$ in cultured population, With reference to bandsharing values and banding patterns, wild population was considerably more diverse than cultured population. Knowledge of the genetic diversity of crucian carp should help in formulating more effective strategies for managing this aquacultural fish species.

• Genomics & Informatics
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• 제10권3호
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• pp.133-144
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• 2012

Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.

• Asian-Australasian Journal of Animal Sciences
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• 제31권8호
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• pp.1078-1087
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• 2018

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD ($r^2$) of 3.698 million SNP pairs was $0.135{\pm}0.204$. The mean $r^2$ decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the $r^2$ calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (${\pm}$standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

• Animal Bioscience
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• 제37권7호
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• pp.1168-1176
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• 2024

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

• 한국양식학회지
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• 제17권1호
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• pp.12-23
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• 2004

Genomic DNAs were extracted from the muscle of twenty-two specimens of two shortnecked clam, Ruditapes phifippinarum populations collected in Anmyeondo and Seocheon. Genetic differences within and between populations were analysed by random amplified polymorphic DNAs-polymerase chain reaction (RAPD-PCR) using twenty arbitrary decamer primers. Out of 20 primers, 6 generated a total of 1,111 major and minor RAPD bands from individuals of two sites, producing approximately 4.2 average polymorphic bands per primer in individuals from Anmyeondo and ranging in size from less than 50 to larger than 1,500 base pairs (bp). The electrophoretic analysis of RAPD products amplified showed moderate levels of similarity among the different individuals in Seo-cheon population. The average bandsharing values (BS value) of the samples within population from Anmyeondo ranged from 0.155 to 0.684, whereas it was 0.143∼0.782 within population from Seocheon. The average BS value between individuals No. 13 and No. 14 from Seocheon was 0.782 which was higher than that of those from Anmyeondo. The single linkage dendrogram resulted from three primers (OPA-08, -09 and -20), indicating six genetic groupings composed of group 1 (No.4, 8 and 10), group 2 (No. 18), group 3 (No.2, 5 and 7), group 4 (No. 1, 3, 6, 9, 11, 12, 13, 14, 15 and 17), group 5 (16, 19 and 20) and group 6 (No. 21 and 22). In the Seocheon population, the individual No. 18 clustered distinctly from the others of this population. The observed genetic distance between the two populations from Anmyeondo and Seocheon was more than 0.209 (0.247 and 0.275). The shortest genetic distance (0.094) displaying significant molecular differences was between individuals No. 13 and No. 14. Especially, the genetic distance between individuals No. 22 and the remnants among individuals in two geographical populations was highest (0.275). This result illustrated that individual No.22 is distinct from other individuals within two shortnecked populations. The different geographical features of two sites may have caused the genetic diversity in two shortnecked clam populations.

• 한국환경과학회지
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• 제3권4호
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• pp.297-304
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• 1994

The genetic variabilities of second chromosomes concealed Sasang natural and experimental populations of Drosophila melanogaster have been analyzed. The experimental population was composed of D. melanognter which had the lethal-free second chromosome collected from Sasang natural population in 1982. The results were as follow; The mean frequencies of deleterious genes were estimated % be 33.33% in Sasang natural population and 31.72% in experimental population. The allelism rates in lethal genes isolated from the natural and experimental populations were calculated to be about 0.95% and 12.28%, respectively. The allelism rates between lethal genes isolated from the natural population and those of the experimental population were calculated to be about 0.01%. The mean values of elimination by frequencies of deleterious genes and allelism rates were 0.0011 in the natural population and 0.0124 in the experimental population. The frequencies of phenotypic sterility of males in the natural and experimental populations were estimated to be 1.49% and 1.36%, respectively. The frequencies of genotypic sterility of females and males were estimated to be 0.90% and 1.80% in the natural population, and that of males was 2.38% in the experimental population.

• Journal of Forest and Environmental Science
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• 제28권4호
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• pp.242-246
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• 2012

The variation in random amplified polymorphic DNA (RAPD) markers were examined for Xanthoceras sorbifolium Bunge seeds from three plantations (Inner Mongolia [IM], Liaoning [LN], and Shandong [SD] province) in China. Mean genetic variation was measured by polymorphism percentage (42.10%) and expected heterozygosity (He=1.27). Among three populations, Shandong showed the highest values both in polymorphism percentage and heterozygosity (p=57.89; Ho=1.58; and He=1.37). Total genetic diversity value, based on the total loci, was estimated as total genetic diversity of the species (Ht)=0.27 and mean within-population genetic diversity (Hs)=0.16. UPGMA cluster analysis showed the genetic closeness between Inner Mongolia and Liaoning population, but that Shandong seems to be the separate population.

• 생명과학회지
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• 제18권7호
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• pp.1015-1018
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• 2008

본 연구는 2007년 3월 가막만에서 양식하고 있는 참굴 34마리를 대상으로 미토콘드리아COI gene 염기서열분석을 통하여 유전자 집단을 조사했다. PCR 증폭에 사용된 primer는 HCO2918과 LCO1491로 product는 658 bp였다. 유전자 배열 결과 가막만 참굴 집단에서 CR1, CR2, CR3, CR4 4개의 haplotype이 나타났다. 그 중 CR3 haplotype이 73% 발생되어 가장 높은 빈도율을 보였다. 계층구조에서도 가막산 참굴은 남해안산과 유전적 유연관계를 보이나, 유전적 거리는 남해안 및 서해안과도 마이너스 값을 보이며 통계적으로도 유전적으로 하나의 집단을 형성하고 있음을 알 수 있다.

• Animal cells and systems
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• 제4권1호
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• pp.39-44
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• 2000

To assess the genetic diversity and population structure of Korean K. borealis, allozyme analysis was performed. The average genetic variability of Korean K. borealis populations was %P=13.2, Ho=0.048, and He=0.045. This value was the lowest in comparison with other Korean amphibian species studied. Also, the value was much lower than that of a reference population from Chinese K. borealis (%P=50, Ho=0.125, He=0.172). Wright's F-statistics showed that Korean K. borealis has distinctly low level of gene flow among regional populations (F$_{ST}$=0.339, Nm=0.487) in comparison with other Korean amphibian species studied. However, the average level of genetic divergence among Korean K. borealis populations was moderate (Nei's D=0.020). Therefore, it appeared that low levels of genetic diversity (He=0.045) and gene flow (Nm=0.487) among regional populations ave probably due to the results of decreasing population size and patchy distribution of this species in Korea.