• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.7
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• pp.658-668
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• 2006

The objective of this study was to develop a technique for the cultivar discrimination using SSR markers in soybean. A total of 91 soybean cultivars developed from 1913 to 2002 in Korea were evaluated by five polymorphic SSR markers (Sat_043, Sat_036, Sat_022, Sat_088 and Satt045). Five SSR markers generated a total of 64 alleles and the number of alleles for each SSR marker ranged from 10 to 15 with average of 12.8. Polymorphic information contents (PIC) by five markers of 91 cultivars were ranged from 0.790 to 0.905 with average of 0.857. A total of 82 cultivars (90%) among 91 soybean cultivars could be individually discriminated by combination of five SSR markers through five step analysis. A cultivar, Buseok, by Sat_043 at the first step, 34 cultivars including Hojangkong by Sat_036 at the second step, 29 cultivars including Dankyeongkong by Sat_022 at the third step, 12 cultivars including Sinpaldalkong 2 by Sat_088 at the fourth step, and 6 cultivars including Saebyeolkong by Satt045 at the fifth step were discriminated. Soybean cultivars which were not discriminated by SSR markers could be discriminated by morphological characteristics.

• Journal of Species Research
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• v.1 no.2
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• pp.224-231
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• 2012

To assess the genetic diversity of Aconitum coreanum (Ranunculaceae) populations in Korea, we have amplified and sequenced eight organellar marker regions, and developed and analyzed microsatellite markers. No sequence variation was detected from the eight organellar markers. Ten microsatellites were developed using Next Generation Sequencing and two microsatellite markers, AK_CA03 and AK_CT07, were identified polymorphic and applied for 143 individuals of twelve A. coreanum populations. Four and five alleles were detected for the two microsatellite loci, respectively, and number of migrants ($N_m$) was estimated as 1.12586. Two microsatellite marker loci showed $F_{ST}$ of 0.205 and 0.275, respectively. The heterozygosity deficit, low level of among-population differentiation, small size of gene flow, and lack of sequence variation of the organellar markers suggest that A. coreanum is reproductively isolated from other Aconitum species and there has been continuous gene flow among the populations of A. coreanum or it has dispersed relatively recently after speciation. Though population pairwise $F_{ST}$'s presented significant geographic structure, further sampling and study will be necessary to confirm this.

• Korean Journal of Plant Taxonomy
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• v.47 no.1
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• pp.6-10
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• 2017

Microsatellite markers were isolated for Daphne kiusiana var. kiusiana (Thymelaeaceae), an evergreen broad-leaved shrub endemic to Korea and Japan. Because its populations in Jeju Island are morphologically controversial, and consistently threatened by anthropogenic pressures, taxonomic delimitation and conservation effort are required at the genetic level. We developed 21 polymorphic microsatellite loci from Next Generation Sequencing data. The primer set included di-, tri-, and tetra-nucleotide repeats. Variability in the markers was tested for 80 individuals of D. kiusiana from three natural populations in Jeju Island and Japan. Among the 21 loci, three were unavailable for population JKJU of Japan. The Neighbor-Joining tree based on microsatellite markers described here classified the three populations into two groups according to geographical or morphological traits. These will be a powerful genetics tool for determining the taxonomic boundary and establishing suitable conservation strategies for D. kiusiana in Jeju Island.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.265-272
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• 2011

This study is to generate SCARs markers for identification of Perilla species. A SCAR is a genomic DNA fragment at a single genetically defined locus that is identified by PCR amplification using a pair of specific oligonucleotide primers. We derived SCARs by sequencing and cloning the both ends of the amplified products of RAPD markers. Sixteen sequence-specific primers were synthesized from eight RAPD markers, which were completely sequenced. We developed the species-specific SCAR markers which could be used successfully in detecting genetic variation in four Perilla species. These markers could be used to verify species-origins of various forms of Perilla germplasms.

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.397-402
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• 2009

Self-incompatibility (SI) prevents self-fertilization by inhibiting the pollen tube growth of self-pollen. Molecular analysis has revealed that the S locus comprises a number of genes, such as the S-locus glycoprotein (SLG), the S-locus receptor kinase (SRK), and SP11 (SCR). Although molecular markers related to those genes have been developed, a simple S-haplotype detecting method has not been reported due to the highly polymorphic and relatively small coding regions. In this study, the sequence characterized amplified region (SCAR) markers were used to establish an efficient radish genotyping method. We identified the S-haplotypes of 192 radish accessions using 19 different markers, which proved to be highly reliable. The accessions were assigned to 17 types of S-haplotypes, including 8 types of SRKs and 9 types of SLGs. Since the developed SCAR markers are based on their gene sequences, we could easily identify the S-haplotypes by a single specific band, with the highest frequencies detected for SLG 5, SRK 1, and SLG 1, in order. Among the tested markers, the SLG 1, SRK 1, and SRK 5 markers exhibited high reliability, compared to phenotypic results. Furthermore, we identified the seven types of unreported SLGs using SLG Class -I and -II specific markers. Although the developed SCAR markers still need to be improved for the genotyping of all S-haplotypes, these markers could be helpful for monitoring inbred lines, and for developing the MAS in radish breeding programs.

• Journal of Life Science
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• v.20 no.7
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• pp.983-990
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• 2010

Genus Spiraea is a woody species primarily distributed throughout Asia. Many species of this genus are important plants medicinally and ecologically. I evaluated a representative sample of the sixteen taxa with random amplified polymorphic DNA (RAPD) markers to estimate genetic relationships within genus Spiraea. In addition, RAPD analysis was also conducted to estimate the genetic diversity and population structure of these species. As the typical populations of Spiraea were small, isolated, and patchily distributed for natural populations, they maintained a low level of genetic diversity for polymorphic primers. The mean H was 0.117 across species. The Korean endemic species (S. chartacea) and patchily distributed species (S. betulifolia) showed fewer alleles per locus (mean 1.240 vs. 1.297), lower percent polymorphic locus (24.0 vs. 29.7), and lower diversity (0.092 vs. 0.121) than a relatively widely spread species. An assessment of the proportion of diversity present within species, $H_{POP}/H_{SP}$, indicated that about 87.8% the total genetic diversity was among species. Thus, the majority of genetic variation (87.8%) resided within species. The phylogenic tree showed three distinct groups. One clade includes S. prunifolia for. simpliciflora, S. thunbergii, S. chamaedryfolia var. ulmifolia, S. media, and S. cantoniensis. Another clade includes S. blumei, S. pubescens, S. chartacea, and S. chinensis. The other clade is the remaining seven species.

• Journal of Life Science
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• v.18 no.4
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• pp.435-440
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• 2008

Random amplified polymorphic DNA (RAPD) markers were used to identify the genetic diversities among and within varieties and landraces of Rehmannia glutinosa. Polymorphic and reproducible bands were produced by 10 primers out of total 20 primers used in the experiment. In RAPD analysis of the 11 genotypes, 64 fragments out of 73 amplified genomic DNA fragments were polymorphic which represented an average 6.4 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 2 (OPA-1) to 13 (OPA-11) and varied in size from 200 bp to 1,400 bp. Especially, OPA-10, OPA-11 and OPA-19 primers showed specific bands for varieties of Korea Jiwhang and Jiwhang il ho, which could be useful for discriminating from other varieties and landraces of R. glutinosa. Percentage polymorphism ranged from a minimum of 50% (OPA-1) to a maximum of 100% (OPA-11), with an average of 87.7%. Similarity coefficients were higher in the genotypes of Korea Jiwhang and Jiwhang il ho than in other populations. In cluster analysis, genotypes of Korea Jiwhang, Jiwhang il ho, and Japanese accession were separated from those of other varieties and landraces. Average of genetic diversity within the population $(H_S)$ was 0.110, while average of total genetic diversity $(H_T)$ was 0.229. Across all RAPD makers the $G_{ST}$ value was 0.517, indicating that about 52% of the total genetic variation could be explained by RAPDs differences while the remaining 48% might be attributable to differences among samples. Consequently, RAPD analysis was useful method to discriminate different populations such as domestic varieties and other landraces. The results of the present study will be used to understand the population and evolutionary genetics of R. gllutinosa.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.9
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• pp.1234-1239
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• 2006

Murrah and NiliRavi are the important North Indian buffalo breeds occupying the prominent position of being the highest milk producers. These breeds are more or less similar at morphological as well as physiological levels. The technique of RAPD-PCR was applied in the present study to identify a battery of suitable random primers to detect genetic polymorphism, elucidation of the genetic structure and rapid assessment of the differences in the genetic composition of these two breeds. A total of 50 random primers were screened in 24 animals each of Murrah and NiliRavi buffaloes to generate RAPD patterns. Of these, 26 (52%) primers amplified the buffalo genome generating 263 reproducible bands. The number of polymorphic bands for the 26 chosen RAPD primers varied from 3 (OPG 06 and B4) to 26 (OPJ 04) with an average of 10.1 bands per primer and size range of 0.2 to 3.2 kb. DNA was also pooled and analyzed to search for population specific markers. Two breed specific RAPD alleles were observed in each of Murrah (OPA02 and OPG16) and NiliRavi (OPG09) DNA pools. RAPD profiles revealed that 11 (4.2%) bands were common to all the 48 individuals of Murrah and NiliRavi buffaloes. Pair-wise band sharing calculated among the individual animals indicated considerable homogeneity of individuals within the breeds. Within breed, band sharing values were relatively greater than those of interbreed values. The low genetic distance (Nei's) value (0.109) estimated in this study is in accordance with the origin and geographical distribution of these breeds. The RAPD analysis indicated high level of genetic similarity between these two important North Indian buffalo breeds.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.683-692
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• 2010

Morphologically, nine different slow-growing protoclones were screened from regenerated protoplasts of heterokaryotic Agaricus bisporus. As such, the present study is the first report on differentiating homo- and heterokaryotic protoclones using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Among 80 primers tested, the seven ISSR and seven RAPD primers selected for the analysis generated a total of 94 ISSR and 52 RAPD fragments, respectively. The ISSR fingerprinting also detected more polymorphic loci (38.29%) than the RAPD fingerprinting (34.61%). A principal coordinate analysis (PCA) was employed to evaluate the resolving power of the markers as regards differentiating protoclones. As a result, the mean polymorphism information content (PIC) for each marker system (i.e., 0.787 for RAPD and 0.916 for ISSR) suggested that ISSR is more effective for determining polymorphisms. The dendrograms constructed using RAPD, ISSR, and an integrated RAPD and ISSR marker system were highly correlated with one another as revealed by a high Mantel correlation (r= 0.98). The pairwise similarity index values also ranged from 0.64 to 0.95 (RAPD), 0.67 to 0.98 (ISSR), and 0.67 to 0.98 (RAPD and ISSR), whereas the mean similarity index values of 0.82, 0.81, and 0.84 were obtained for the RAPD, ISSR, and combined data, respectively. As there was a good correspondence between the RAPD and ISSR similarity matrices, ISSR would appear to be an effective alternative to RAPD in the genetic diversity assessment and accurate differentiation of homo- and heterokaryotic protoclones of A. bisporus.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.75-81
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• 2017

A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.