• Mycobiology
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• v.45 no.2
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• 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 CROP SCIENCE
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• v.63 no.1
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• pp.1-7
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• 2018

Information on the patterns of genetic diversity and population structure is essential for the rational use and efficient management of germplasms; accurate information aids in monitoring germplasms, and can also be used to predict potential genetic gains. In this study, we assessed genetic diversity, focusing on Korean rice accessions for theand their sustainable conserved diversity. Using DNA profiling with 12 simple sequence repeat (SSR) markers, we detected a total of 333 alleles among 2,016 accessions. The number of alleles ranged from 21 to 53, with an average of 27.8. Average polymorphism information content was 0.797, with the lowest being 0.667 and the highest 0.940. CA cluster analysis and the model-based population structure revealed two main groups that could be subdivided into five subgroups. Analysis of the molecular variance study based on the SSR profile data showed 5% variance among the profiles, whereas we recorded 93% variance among individuals and 2% variance within individuals. Specifically, the utilized diversity for of the breeding program is restricted in that cultivars were located in limited clades. These results revealed that preserving the diversity of Korean landraces could be useful sources for breeding new rice cultivars, and cwould be the basis for the sustainable conservation and utilization of a Korean rice germplasm.

• Horticultural Science & Technology
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• v.29 no.6
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• pp.600-609
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• 2011

One hundred twenty two accessions of 6 species in genus Allium were collected throughout 5 regions of Korea. Their genetic relationship was investigated by using inter simple sequence repeat (ISSR) markers. The morphological analysis was measured for 6 quantitative and quantified for 1 qualitative trait. ISSR analysis obtained a total of 370 polymorphic bands by using seventeen primers. The cluster analysis of genus Allium based on morphological data could identify three groups. The accessions of Allium belonged to the Allium monanthum clustered into five groups at genetic distance ranging from 0.94 on the base of ISSR analysis. Correlation analysis between morphological and ISSR analysis showed low coefficient(r = 0.036). These markers are thought to be used in research of molecular markers for classification and cross breeding of Allium monanthum and A. grai.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.23-23
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• 2017

Rice (Oryza sativa L.) is the world's most important cereal crop. In crop plant, chlorophyll content and leaf senescence could affect grain filling and yield. We analyzed a QTL associated with chlorophyll content and delayed leaf senescence using high chlorophyll near isogenic line (HC-NIL). HC-NIL derived from a cross between Oryza sativa cv. Hwaseong as a recurrent parent and wild species O. grandiglumis as a donor parent showed higher chlorophyll content than Hwaseong. To identify QTL associated with chlorophyll content, 58 $F_3$ and 38 $F_4$ lines were developed from a cross between HC-NIL and Hwaseong. For QTL analysis, simple sequence repeat (SSR) markers were used for genotyping and one-way ANOVA was conducted. A QTL for chlorophyll content (qCC2) was detected in chromosome 2 and explained 24.63% of phenotypic variation. The senescence effect of the qCC2 was examined in dark-induced incubation (DII). Detached leaves from Hwaseong and HC-NIL were incubated on 3mM MES buffer (pH 5.8) at $27^{\circ}C$ under complete dark condition. After 3 days of incubation, the Hwaseong leaves turned yellow, but the HC-NIL leaves were green. HC-NIL has higher chlorophyll content with delayed senescence than Hwaseong. These results indicated that qCC2 is associated with stay-green phenotype. To know whether the qCC2 is responsible for leaf functionality, ion leakage test and Fv/Fm measurement were performed. Both experiment results showed that differences were observed between Hwaseong and HC-NIL but it was not statistically significant. These results might suggest that the qCC2 is possibly related to chlorophyll content and non-functional stay-green phenotype.

• Journal of Animal Science and Technology
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• v.55 no.2
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• pp.87-93
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• 2013

We identified four new bovine tri-nucleotide microsatellite loci and analyzed their sequence structures and genetic parameters in 105 randomly selected Korean cattle (Hanwoo). Allele numbers of the loci B17S0808, B15S6253, B8S7996, and B17S4998 were 10, 11, 12, and 29, respectively. These alleles contained a simple or compound repeat sequences with some variations. Allele distributions of all these loci were in Hardy-Weinberg equilibrium (P > 0.05). Observed heterozygosity and expected heterozygosity ranged from 0.54 (B15S6253) to 0.92 (B17S4998) and from 0.599 (B15S6253) to 0.968 (B17S4998), respectively, and two measures of heterozygosity at each locus were highly correlated. Polymorphism information content (PIC) for these 4 loci ranged from 0.551 (B15S6253) to 0.932 (B17S4998), which means that all these loci are highly informative (PIC > 0.5). Other genetic parameters, power of discrimination (PD) and probability of exclusion (PE) ranged from 0.783 (B15S6253) to 0.984 (B17S4998) and from 0.210 (B15S6253) to 0.782 (B17S4998), respectively. Their combined PD and PE values were 0.9999968 and 0.98005176, respectively. Capillary electrophoresis revealed that average peak height ratio for a stutter was 13.89% at B17S0808, 26.67% at B15S6253, 9.09% at B8S7996, and 43.75% at B17S4998. Although the degree of genetic variability of the locus B15S6253 was relatively low among these four microsatellite markers, their favorable parameters and low peak height ratios for stutters indicate that these four new tri-nucleotide microsatellite loci could be useful multiplex PCR markers for the forensic and population genetic studies in cattle including Korean native breed.

• Journal of Plant Biotechnology
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• v.43 no.3
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• pp.367-375
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• 2016

In the present study, we conducted genetic characterization of 90 commercial maize varieties and parental lines using microsatellite markers. Thirteen microsatellite markers were selected from 100 primer pairs in the maize genome data on the basis of polymorphism information contents (PIC) value and distinct amplification products. These markers detected 5 to 24 alleles, with an average of 13.69. The mean PIC value was 0.865 and ranged from 0.716 to 0.942. The unweighted pair-group method with arithmetical average (UPGMA) analysis was conducted for constructing the dendrogram using Jaccard's genetic similarity coefficient. The genetic similarity varied from 0.07 to 0.824. Thirteen microsatellite markers identified all 90 maize varieties and parental lines. The maize varieties were clustered into 5 major groups consistent with type and pedigree information. The microsatellite profile database of maize varieties could be used to select comparative varieties through genetic relationship analysis between existing varieties and candidate varieties in distinctness tests.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.108-120
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• 2017

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene ${\beta}$ - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.243-248
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• 2008

The bean bug Riptortus clavatus Thunberg (Heteroptera: Alydidae) is an important pest, causing serious yield loss in soybean. But the information on mechanism of resistance to R. clavatus is limited. The objective of this study was to identify QTLs for R. clavatus resistance using simple sequence repeat (SSR) markers in a soybean population of recombinant inbred lines (RILs) developed from the cross PI 171451 ${\times}$ Hwaeomputkong. A genetic map from this population was constructed with a total of 136 SSR markers covering 1073.9 cM on 20 linkage groups (LGs). With 126 $F_5$ RILs, two independent QTLs for resistance to R. clavatus were mapped on LGs B1 and C2. The amount of phenotypic variation explained by these QTLs ranged from 12 to 16%. PI 171451 showed an escape response to R. clavatus. Under feeding conditions, 14.4% of RILs showed greater resistance to R. clavatus than the resistant parent. The resistance to R. clavatus in soybean from PI 171451 was incomplete and quantitatively inherited and the QTLs for resistance to R. clavatus detected in the RIL population were not significantly affected by epistatic interactions.

• Journal of Life Science
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• v.14 no.2
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• pp.339-344
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• 2004

Identification of individual quantitative trait loci (QTL) is a prerequisite to application of marker-assisted selection for stern length. Two simple sequence repeat (SSR)-based linkage maps were constructed from recombination inbred line populations between cross of Keunolkong and Shinpaldalkong. Two parents used differed greatly in stem length, which were 30.57 cm and 49.75 cm in Keunolkong and Shinpaldalkong, respectively. Using the constructed maps, regression analysis and interval mapping were performed to identify QTLs conferring stem length. Four QTLs for stem length on linkage groups (LG) F, J, N and O were identified in the Keunolkong ${\times}$ Shinpaldalkong population and they totally explained 37.83% of variation for stem length. In the population, two major QTLs on LG J and O conditioning 14.25% and 10.68% of the phenotypic variation in stem length were determined and two QTLs with minor effect were detected on LG F and N. Identification of QTLs for stem length and mapping individual locus should facilitate to describe genetic mechanisms for stem length in different population. SSR markers tightly linked to QTLs for stem length allow to accelerate the elimination of deleterious genes and selection for desirable recombinants at early stage in crop breeding programs.