• Asian-Australasian Journal of Animal Sciences
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• v.27 no.7
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• pp.926-931
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• 2014

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The $F_{IS}$ values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was $9.87{\times}10^{-14}$ in population J, $3.17{\times}10^{-9}$ in population B, and $1.03{\times}10^{-12}$ in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.466-472
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• 2016

This study analyzed the genetic diversity of 115 pear germplasms using 15 SSR markers. Three to forty-one SSR alleles were detected for each locus with an average of 16 alleles per locus. The average availability of markers was 0.966. The average observed heterozygosity ($H_{obs}$) was 0.603 (range: 0.140 to 0.929). The average expected heterozygosity ($H_{exp}$) was 0.718 (range: 0.463 to 0.904). The average polymorphism information content (PIC) was 0.692 (range: 0.403 to 0.897). The genetic relationships of pear germplasms were classified into two major groups by geographic origins and genetic characteristics according to genetic distance. The first group was composed of European pear belonging to Pyrus communis. The second group consisted of P. pyrifolia, P. ussuriensis, P. bretschneideri, P. betulaefolia, P. calleryana, interspecific hybrids, and unclear germplasms. The results of this study suggest that genotype analysis of pear germplasms using SSR markers can identify the genetic diversity of germplasms, and can be used to provide basic information for pear breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.323-333
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• 2013

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright's F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.853-863
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• 2014

This study was carried out to construct a DNA profile database of 100 strawberry cultivars using microsatellite markers. Two hundred seventy four microsatellite primer pairs were screened with a set of 21 strawberry cultivars with different morphological traits. Twenty five primer pairs were selected because they produced reliable and reproducible fingerprints. These primer pairs were used to develop DNA profiles of 100 strawberry cultivars. Three to thirteen alleles were detected by each marker with an average of 7.50. The average polymorphism information content varied from 0.331 to 841 (average 0.706). Cluster analysis showed that the 100 cultivars were divided into 7 major groups reflecting geographic origin and pedigree information. Moreover, most of the cultivars could be discriminated by marker genotypes. These markers will be useful as a tool for the protection of plant breeders' intellectual property rights in addition to providing the means to intervene seed disputes relating to variety authentication.

• Journal of Life Science
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• v.16 no.6
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• pp.1001-1005
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• 2006

The objective of this study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for genetic diversity assessment and identification of rice varieties. The 23 primers selected from 50 SSR primers showed polymorphisms in the 21 rice varieties. The 2 to 9 SSR alleles were detected for each locus with an average of 3.00 alleles per locus. The polymorphism information content (PIC) ranged form 0.091 to 0.839. Based on band patterns, UPGMA cluster analysis was conducted. These varieties were separate into 4 groups corresponding to rice ecotype and pedigree information and genetic distance of cluster ranging from 0.59 to 0.92. The 4 SSR primer sets (RM206, RM225, RM418, RM478) selected form 23 polymorphic primers were differentiated all the rice variety from each other by markers genotypes. These markers may be used wide range of practical application in variety identification of rice.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.142-153
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• 2016

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.77-86
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• 2015

Chicken is one of the major livestock, especially for supplying proteins to human. The chicken genome size is approximately one-third compared with that of the human genome and regarded as a valuable model animal for genetics and development biology. In this study, we constructed the genetic linkage map for Korean native chicken (KNC) using 131 microsatellite (MS) and 8 single nucleotide polymorphism (SNP) markers. As a result, the total map length was calculated as 2729.4 cM and the average genetic distance between markers was 19.64 cM. The marker orders and genetic distances were well matched with the consensus linkage map except for the physical order of ADL0278 and MCW0351 in GGA8. In addition, the recombination rates in marcrochromosomes were 3.7 times higher than that of microchromosomes. The average numbers of alleles, expected heterozygosity (Hexp) and polymorphic information content (PIC) values were calculated as 5.5, 0.63 and 0.58, respectively. These results will give useful information for the understanding of genetic structure and QTL studies in KNC.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.15-26
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• 2015

In this study, genotyping was executed by using 27 microsatellite markers for genetic diversity of 469 Korean Native Chickens [20 population, each population is 24 samples but Hanhyup A line is 13 samples). in total 469 samples were collected from National Institute of Animal Science (Korean Native Chicken (NR, NY, NG, NL and NW), Ogye (NO), Leghorn F,K (NF and NK), Black and Brown cormish (NH and NS), Rhode Island Red C, D (NC and ND), Total is 12 populations] and Hanhyup [H line (HH), F line (HF), G line (HG), V line (HV), S line (HS), W line (HW), Y line (HY), A line (HA), total is 8 populations]. [The allele number were observed 5 (ADL0268) to 20 (MCW0127) each markers. Observed heterozygostiy ($H_{obs}$), expected heterozygosity ($H_{exp}$), polymorphism Information Content (PIC) were observed 0.359 to 0.677, 0.668 to 0.881 and 0.646 to 0.869, respectively. Using these markers, the calculated the heterozygote deficit within chicken line ($F_{is}$) value each population from mean 0.117. Phylogenetic tree showing the genetic relationship among 20 population using standard genetic distance calculated from 27 microsatellite markers. genetic distances revealed the closest (0.175) between NC and ND. on the other hand, Farthest genetic distances (0.710) revealed between NF and HV. STRUCTURE analysis and Principal Components Analysis (PCA) showed that results of similar phylogenetic tree. The expected probability of identity values on random individuals (Total population and only Hanhyup line) was estimated at $8.80{\times}10^{-83}$ and $3.87{\times}10^{-117}$, respectively. In conclusion, This study shows the useful data that be utilized as a basic data of Korean Native Chicken breeding and development for commercial chicken industry to meet the consumer's demand.

• Journal of Mushroom
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• v.15 no.2
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• pp.78-83
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• 2017

Microsatellite SSR markers were developed and utilized to reveal the genetic diversity of 32 strains of Flammulina velutipes collected in Korea, China, and Japan. From the SSR-enriched library, 490 white colonies were randomly selected and sequenced. Among the 490 sequenced clones, 85 (17.35%) were redundant. Among the remaining 405 unique clones, 201 (49.6%) contained microsatellite sequences. We used 12 primer pairs that produced reproducible polymorphic bands for four diverse strains, and these selected markers were further characterized in 32 Flammulina velutipes strains. A total of 34 alleles were detected using the 12 markers, with an average of 3.42 alleles, and the number of alleles ranged from two to seven per locus. The major allele frequency ranged from 0.42 (GB-FV-127) to 0.98 (GB-FV-166), and values for observed ($H_O$) and expected ($H_E$) heterozygosity ranged from 0.00 to 0.94 (mean = 0.18) and from 0.03 to 0.67 (mean = 0.32), respectively. SSR loci amplified with GB-FV-127 markers gave the highest polymorphism information content (PIC) of 0.61 and mean allele number of five, whereas for loci amplified with GB-FV-166 markers these values were the lowest, namely 0.03 and two. The mean PIC value (0.29) observed in the present study with average number of alleles (3.42). The genetic relationships among the 32 Flammulina velutipes strains on the basis of SSR data were investigated by UPGMA cluster analysis. In conclusion, we succeeded in developing 12 polymorphic SSRs markers from an SSR-enriched library of Flammulina velutipes. These SSRs are presently being used for phylogenetic analysis and evaluation of genetic variations. In future, these SSR markers will be used in clarifying taxonomic relationships among the Flammulina velutipes.

• Journal of Ginseng Research
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• v.44 no.4
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• pp.637-643
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• 2020

Background: Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.