• Korean Journal of Food Science and Technology
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• v.40 no.6
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• pp.603-610
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• 2008

The principal objective of current study was to evaluate the potential of near infrared reflectance spectroscopy (NIRS) as a non-destructive method for the prediction of the amylose and protein contents of un-hulled and brown rice in broad-based calibration models. The average amylose and protein content of 75 rice accessions were 20.3% and 7.1%, respectively. Additionally, the range of amylose and protein content were 16.6-24.5% and 3.8-9.3%, respectively. In total, 79 rice germplasms representing a wide range of chemical characteristics, variable physical properties, and origins were scanned via NIRS for calibration and validation equations. The un-hulled and brown rice samples evidenced distinctly different patterns in a wavelength range from 1,440 nm to 2,400 nm in the original NIR spectra. The optimal performance calibration model could be obtained by MPLS (modified partial least squares) using the first derivative method (1:4:4:1) for un-hulled rice and the second derivative method (2:4:4:1) for brown rice. The correlation coefficients $(r^2)$ and standard error of calibration (SEC) of protein and amylose contents for the un-hulled rice were 0.86, 2.48, and 0.84, 1.13, respectively. The $r^2$ and SEC of protein and amylose content for brown rice were 0.95, 1.09 and 0.94, 0.42, respectively. The results of this study suggest that the NIRS technique could be utilized as a routine procedure for the quantification of protein and amylose contents in large accessions of un-hulled rice germplasms.

• Horticultural Science & Technology
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• v.31 no.6
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• pp.772-781
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• 2013

The objective of this study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (EST) of lettuce (Lactuca sativa) and identify 9 germplasms from 3 wild species of lettuce and 61 commercial cultivars using the developed EST-SSR markers. A total of 81,330 lettuce ESTs from NCBI databases were used to search for SSR and 4,229 SSR loci were identified. The highest proportion (59.12%, 2500) was represented by trinucleotide, followed by dinucleotide (29.70%, 1256) and hexanucleotide (6.62%, 280) among SSR repeat motifs. Totally 474 EST-SSR primers were developed from EST and a random set of 267 primers was used to assess the genetic diversity among 9 germplasms and 61 cultivars. Out of 267 primers, 47 EST-SSR markers showed polymorphism between 7 cultivars. Twenty-six EST-SSR markers among 47 EST-SSR markers showed high polymorphism, reproducibility, and band clearance. The relationship between 26 markers genotypes and 70 accessions was analyzed. Totally 127 polymorphic amplified fragments were obtained by 26 EST-SSR markers and two to nine SSR alleles were detected for each locus with an average of 4.88 alleles per locus. Average polymorphism information content was 0.542, ranging from 0.269 to 0.768. Genetic distance of clusters ranged from 0.05 to 0.94 between 70 accessions and dendrogram at a similarity of 0.34 gave 7 main clusters. Analysis of genetic diversity revealed by these 26 EST-SSR markers showed that the 9 germplasms and 61 commercial cultivars were discriminated by marker genotypes. These newly developed EST-SSR markers will be useful for cultivar identification and distinctness, uniformity and stability test of lettuce.

• Korean Journal of Plant Resources
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• v.32 no.5
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• pp.519-542
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• 2019

Twenty soybean cultivars developed recently were assessed using 27 insertion and deletion (InDel) markers derived from dense variation blocks (dVBs) of soybean genome. The objective of this study is to identify the distinctness and genetic relationships among a total of 169 soybean accessions including new cultivars. The genetic homology between 149 accessions in the soybean barcode system and 20 new cultivars was 61.3% on average with the range from 25.9% to 96.3%, demonstrating the versatile application of these markers for cultivars identification. The phylogenic analysis revealed four subgroups related to their usage. The 80% of cultivars for vegetable and early maturity and the 65.9% of cultivars for bean sprouts were clustered in subgroup I-2 and II-2, respectively, indicating of the limited gene pools of their crossing parents in breeding. On the other hands, the cultivars for soy sauce and tofu with considerable gene flow by genome reshuffling were distributed evenly to several subgroups, I-1 (44.4%), I-2 (26.4%) and II-2 (23.6%). We believe that the 27 InDel markers specific to dVBs can be used not only for cultivar identification and genetic diversity, but also in breeding purposes such as introduction of genetic resources and selection of breeding lines with target traits.

• Korean Journal of Breeding Science
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• v.41 no.1
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• pp.16-24
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• 2009

Although leaf characters are important in soybean [Glycin max (L.) Merr.] breeding and development of cultural methods, very little information has been reported. The objectives of this study were to evaluate and analyze the relationships among leaf characters and suggest possible classification criteria for cultivating and wild (Glycin soja Sieb. & Zucc.) soybeans. Total of 94 cultivating and 91 wild soybean accessions from the Soybean Germplasm Laboratory of Chungbuk National University were used for this study. Central leaflet of the second leaf from the top of the plant was selected to measure leaf characters. Average leaf length, leaf width, leaf area, leaf shape index (LSI) of cultivating and wild soybeans were 12.3$\pm$1.25 cm and 6.6$\pm$1.35 cm, 6.8$\pm$1.241 cm and 2.9$\pm$0.92 cm, 55.6$\pm$15.75 $cm^2$ and 14.3$\pm$7.83 $cm^2$, and 1.9$\pm$0.38 and 2.4$\pm$0.53, respectively. Based on LSI, three categories of leaf shape, i.e., oval, ovate and lanceolate, were defined as LIS$\leq$2.0, LSI 2.1~3.0 and 3.1$\leq$LSI, respectively. Percentage of oval, ovate and lanceolate leaf types among cultivating and wild soybean accessions were 78.7%, 17.0% and 4.3 %, and 40%, 15.4% and 4.4%, respectively. Based on leaf length, three categories for cultivating, i.e. short leaf ($\leq$11.0 cm), intermediate (11.1~13.0 cm), and long (13.1 cm$\leq$), and four categories, i.e. short ($\leq$5.0 cm), intermediate (5.1~7.0 cm), long (7.0~9.0 cm), and very long (9.1 cm$\leq$) for wild soybeans were defined. Short, intermediate and long leaf types were about 1/3, 1/2 and 1/6, respectively, in cultivating soybeans, and 15.4%, 40.7% and 39.5%, plus 4.4% of very long leaf type in wild soybean. Cultivating and wild soybeans had leaf thickness, leaf area ratio (LAR), angle and petiol length of 0.25$\pm$0.054 mm and 0.14$\pm$0.032 mm, 40.1$\pm$8.22 and 53.7$\pm$12.02, $37.6{\pm}5.89^{\circ}$ and $54.6{\pm}10.77^{\circ}$, and 23.9$\pm$5.89 cm and 5.9$\pm$2.33 cm, respectively. There were highly significant positive correlations between leaf length and leaf width, and negative correlation between LSI and leaf width both in cultivating and wild soybeans. Although leaf area showed significant correlations with leaf length, leaf width and LIS in cultivating soybeans, wild soybeans showed no significant relationships among these characters. In general, soybeans with oval, ovate and lanceolate leaves were significantly different in leaf width and thickness. Cultivating soybean with oval leaf had greater leaf area, while wild soybeans with oval or ovate leaf had longer petiol than with lanceolate leaf.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.53 no.spc
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• pp.115-120
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• 2008

Lipid soluble vitamin E consists of tocopherols and tocotrienols depending upon double bonds in phytyl side chains attached to chromanol ring. Recent reports on antioxidative, anticancer, and cholesterol-lowering effects of tocotrienols have increased researches and commercialization of tocotrienols. Purple perilla (Perilla frutescens var. acuta Kudo) has been reported as a plant containing tocotrienols along with tocopherol forms of vitamin E based upon normal phase HPLC analysis. To confirm the existence or absence of tocotrienol form of vitamin E in purple perilla, comparative analysis using HPLC, GC/FID, and GC/MSD has been conducted for 14 purple perilla genetic accessions collected from Korea and Japan. Normal phase HPLC analysis showed ${\alpha}-$, ${\beta}-$, ${\gamma}-$, and ${\delta}-tocopherols$ along with peaks with retention times quite similar to ${\beta}-$ and ${\gamma}-tocotrienols$. Same purple perilla samples, analysed by GC exhibited ${\alpha}-$, ${\beta}-$, ${\gamma}-$, and ${\delta}-tocopherols$ quantitatively equivalent to HPLC results. However, no peaks for ${\beta}-$ and ${\gamma}-tocotrienols$ could be observed and unknown two peaks of similar retention times with ${\beta}-$ and ${\gamma}-tocotrienols$ were identified not corresponding tocotrienols by GC/MSD. These results suggest the absence of tocotrienol form of vitamin E in purple perilla as well as the necessity of using GC-based qualitative and quantitative vitamin E analysis to avoid misinterpretation of peaks with similar retention times as tocotrienol isomers when analysed by an HPLC.

• Molecules and Cells
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• v.26 no.2
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• pp.146-151
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• 2008

The brown planthopper (BPH) is a major insect pest in rice, and damages these plants by sucking phloem-sap and transmitting viral diseases. Many BPH resistance genes have been identified in indica varieties and wild rice accessions, but none has yet been cloned. In the present study we report fine mapping of the region containing the Bph1 locus, which enabled us to perform marker-aided selection (MAS). We used 273 F8 recombinant inbred lines (RILs) derived from a cross between Cheongcheongbyeo, an indica type variety harboring Bph1 from Mudgo, and Hwayeongbyeo, a BPH susceptible japonica variety. By random amplification of polymorphic DNA (RAPD) analysis using 656 random 10-mer primers, three RAPD markers (OPH09, OPA10 and OPA15) linked to Bph1 were identified and converted to SCAR (sequence characterized amplified region) markers. These markers were found to be contained in two BAC clones derived from chromosome 12: OPH09 on OSJNBa0011B18, and both OPA10 and OPA15 on OSJNBa0040E10. By sequence analysis of ten additional BAC clones evenly distributed between OSJNBa0011B18 and OSJNBa0040E10, we developed 15 STS markers. Of these, pBPH4 and pBPH14 flanked Bph1 at distances of 0.2 cM and 0.8 cM, respectively. The STS markers pBPH9, pBPH19, pBPH20, and pBPH21 co-segregated with Bph1. These markers were shown to be very useful for marker-assisted selection (MAS) in breeding populations of 32 F6 RILs from a cross between Andabyeo and IR71190, and 32 F5 RILs from a cross between Andabyeo and Suwon452.

• Journal of Life Science
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• v.20 no.4
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• pp.632-638
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• 2010

The genetic diversity among 48 persimmon (Diospyros kaki Thunb.) accessions, indigenous in Korea and introduced from Japan and China, was evaluated by using simple sequence repeat (SSR) markers. From 20 SSR primer sets, a total of 114 polymorphic markers were detected among 12 pollination-constant non-astringent (PCNA), 13 pollination-variant non-astringent (PVNA), 15 pollination-variant astringent (PVA), and 8 pollination-constant astringent (PCA) cultivars. Analysis of pair-wise genetic similarity coefficient (Nei-Li) and unweighted pair-group method with arithmetic averaging (UPGMA) clustering revealed two main clusters and four subclusters for cluster I. The subclustering pattern was in accordance with the classification of persimmon cultivars based on the nature of astringency loss. Phenetic relationships among the subclusters showed a closer relatedness of the PCNA group with the PVNA group, and the PVA with the PCA group. Genetic similarity co-efficiency was 0.499 on average and the highest (0.954) similarity was observed between 'Cheongdo-Bansi' and 'Haman-Bansi'. The similarity was lowest (0.192) between 'Damopan'and 'Atago'. Identification of each cultivar with the execption of 'Cheongdo-Bansi' and 'Gyeongsan-Bansi' was possible based on the SSR fingerprints, suggesting that these SSR markers are a useful tool for protecting intellectual property on newly developed cultivars.

• Korean Journal of Plant Taxonomy
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• v.42 no.3
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• pp.215-221
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• 2012

Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii.

• Korean Journal of Plant Resources
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• v.26 no.3
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• pp.362-369
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• 2013

Agastache rugosa, a member of the mint family (Labiatae), is a perennial herb widely distributed in East Asian countries. It is used in traditional medicine for the treatment of cholera, vomiting, and miasma. This study assessed the genetic diversity and population structures on 65 accessions of Korean mint A. rugosa germplasm based on inter simple sequence repeat (ISSR) markers. The selected nine ISSR primers produced reproducible polymorphic banding patterns. In total, 126 bands were scored; 119 (94.4%) were polymorphic. The number of bands generated per primer varied from 7 to 18. A minimum of seven bands was generated by primer 874, while a maximum of 18 bands was generated by the primer 844. Six primers (815, 826, 835, 844, 868, and 874) generated 100% polymorphic bands. This was supported by other parameters such as total gene diversity ($H_T$) values, which ranged from 0.112 to 0.330 with a mean of 0.218. The effective number of alleles ($N_E$) ranged from 1.174 to 1.486 with a mean value of 1.351. Nei's genetic diversity (H) mean value was 0.218, and Shannon's information index (I) mean value was 0.343. The high values for total gene diversity, effective number of alleles, Nei's genetic diversity, and Shannon's information index indicated substantial variations within the population. Cluster analysis showed characteristic grouping, which is not in accordance with their geographical affiliation. The implications of the results of this study in developing a strategy for the conservation and breeding of A. rugosa and other medicinal plant germplasm are discussed.

• Weed & Turfgrass Science
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• v.2 no.1
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• pp.15-22
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• 2013

The phenotypic traits of herbicide-tolerant transgenic rice were compared with those of wild type (Dongjin) as well as two accessions (Hwaseong-aengmi 1 and Gwangyang-aengmi 12) of weedy rice. This study was conducted to investigate whether unintentional alterations in phenotypic characteristics occurred in the transgenic rice and whether the altered traits were similar to those in the two weedy rices. All qualitative traits studied were similar in the transgenic or wild-type rice. On the other hand, awn presence, flag leaf attitude and grain color differed considerably between herbicide-tolerant transgenic rice and weedy rice. As for quantitative traits, plant height, the number of tillers per plant and shoot dry weight were significantly greater for weedy rice than transgenic or wild-type rice. Grain weight per plant and 1000-grain weight of transgenic (or wild-type) rice were significantly greater than those of weedy rice. Transgenic rice shattered less than the other rices. Amylose and protein contents in embryos of transgenic rice were significantly different from those of weedy rice. The potential for weediness of the transgenic rice may be assessed using phenotype comparison between transgenic and weedy rice as shown in this study.