• Title/Summary/Keyword: Coefficients of the variation

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Use of Microsatellite Markers to Identify Commercial Melon Cultivars and for Hybrid Seed Purity Testing (Microsatellite Marker를 이용한 멜론 시판품종의 품종식별과 F1 순도검정)

  • Kwon, Yong-Sham;Hong, Jee-Hwa
    • Horticultural Science & Technology
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    • v.32 no.4
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    • pp.525-534
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    • 2014
  • Microsatellite markers were used to identify 58 major commercial melon cultivars, and to assess hybrid seed purity of a melon breeding line known as '10H08'. A set of 412 microsatellite primer pairs were utilized for fingerprinting of the melon cultivars. Twenty-nine markers showed hyper-variability and could discriminate all cultivars on the basis of marker genotypes, representing the genetic variation within varietal groups. Cluster analysis based on Jaccard's distance coefficients using the UPGMA algorithm categorized 2 major groups, which were in accordance to morphological traits. The DNA bulks of female and male parents of breeding line '10H08' were tested with 29 primer pairs based on microsatellites to investigate purity testing of $F_1$ hybrid seeds, and 5 primer pairs exhibited polymorphism. One microsatellite primer pair (CMGAN12) produced unambiguous polymorphic bands among the parents. Among 192 seeds tested with CMGAN12, progeny possibly generated by self-pollination of the female parent were clearly distinguished from the hybrid progeny. These markers will be useful for fingerprinting melon cultivars and can help private seed companies to improve melon seed purity.

Use of Microsatellite Markers Derived from Genomic and Expressed Sequence Tag (EST) Data to Identify Commercial Watermelon Cultivars (수박 시판 품종의 식별을 위한 Genomic과 Expressed Sequence Tag (EST)에서 유래된 Microsatellite Marker의 이용)

  • Kwon, Yong-Sham;Hong, Jee-Hwa;Kim, Du-Hyun;Kim, Do-Hoon
    • Horticultural Science & Technology
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    • v.33 no.5
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    • pp.737-750
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    • 2015
  • This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

Analysis on Spatial Variability of Rainfall in a Small Area (소규모 지역에 대한 강우의 공간변화도 분석)

  • Kim, Jong Pil;Kim, Won;Kim, Dong-Gu;Lee, Chanjoo
    • Journal of Korea Water Resources Association
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    • v.48 no.11
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    • pp.905-913
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    • 2015
  • This study deployed six rain gauges in a small area for a dense network observing rainfall and analyzed the spatial variability of rainfall. They were arranged in a $2{\times}3$ rectangular grid with equal space of 60 m. The rainfall measurements from five gauges were analyzed during the period of 50 days because one was seriously affected by alien substance. The maximum difference in cumulative rainfall from them is approximately 38.5 mm. The correlation coefficients from hourly rainfall time series differ from each other while daily rainfall coincide. The coefficient of variation in hourly rainfall varies up to 224% and that in daily rainfall up to 91%. The results from uncertainty analysis show that with only four rain gauges areal mean rainfall cannot be estimated over 95% accuracy. For reliable flood prediction and effective water management it is required to develop a new technique for the estimation of areal rainfall.

Estimating Groundwater Level Variation due to the Construction of a Large Borrow Site using MODFLOW Numerical Modeling (대규모 토취장 개발 예정 지역의 수치모델을 이용한 지하수위 변동 예측)

  • Ryu, Sanghun;Park, Joonhyeong;Kim, Gyoobum
    • Journal of the Korean GEO-environmental Society
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    • v.13 no.10
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    • pp.15-23
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    • 2012
  • A numerical model and field monitoring data are used to estimate a change in groundwater level at a borrow site, which will be constructed at the mountainous area with a large ground excavation in the study area, Hwaseong city. Lithologic data and hydraulic coefficients are collected at 9 boreholes and also groundwater levels are measured at these boreholes and existing wells in the study area. Additionally, groundwater recharge rate for the type of land cover is estimated using water budget analysis; 133.34mm/year for a mountainous area, 157.68mm/year for a farming area, 71.08mm/year for an urbanized area, and 26.06mm/year for a bedrock exposure area. The change in groundwater level in and around a borrow site is simulated with Modflow using these data. The result of a transient model indicates that a removal of high ground (over 40El.m) by an excavation will produce a decrease in groundwater levels, up to 1 m, around a borrow site in 10 years. It also explains that this ground excavation will bring about the decreases of 9.4% and 7.0% for groundwater recharge and surface runoff, respectively, which are the factors causing groundwater level's change. This study shows that it is required to construct the groundwater monitoring wells to observe the change of groundwater near a borrow site.

Association Analysis of Monocyte Chemotactic Protein-3 (MCP3) Polymorphisms with Asthmatic Phenotypes

  • Park, Byung-Lae;Kim, Lyoung-Hyo;Choi, Yoo-Hyun;Cheong, Hyun-Sub;Park, Hae-Sim;Hong, Soo-Jong;Choi, Byoung-Whui;Lee, June-Hyuk;Uh, Soo-Taek;Park, Choon-Sik;Shin, Hyoung-Doo
    • BMB Reports
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    • v.38 no.1
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    • pp.77-81
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    • 2005
  • The monocyte chemotactic protein-3 (MCP3), on chromosome 17q11.2-q12, is a secreted chemokine, which attracts macrophages during inflammation and metastasis. In an effort to discover additional polymorphism(s) in genes whose variant(s) have been implicated in asthma, we scrutinized the genetic polymorphisms in MCP3 to evaluate it as a potential candidate gene for asthma host genetic study. By direct DNA sequencing in twenty-four individuals, we identified four sequence variants within the 3 kb full genome including 1,000bp promoter region of MCP3; one in promoter region (-420T>C), three in intron (+136C>G, +563C>T, +984G>A) respectively. The frequencies of those four SNPs were 0.020 (-420T>C), 0.038 (+136C>G), 0.080 (+563C>T), 0.035 (+984G>A), respectively, in Korean population (n = 598). Haplotypes, their frequencies and linkage disequilibrium coefficients (|D'|) between SNP pairs were estimated. The associations with the risk of asthma, skin-test reactivity and total serum IgE levels were analyzed. Using statistical analyses for association of MCP3 polymorphisms with asthma development and asthma-related phenotypes, no significant signals were detected. In conclusion, we identified four genetic polymorphisms in the important MCP3 gene, but no significant associations of MCP3 variants with asthma phenotypes were detected. MCP3 variation/haplotype information identified in this study will provide valuable information for future association studies of other allergic diseases.

Construction of a DNA Profile Database for Commercial Cucumber (Cucumis sativus L.) Cultivars Using Microsatellite Marker (Microsatellite 마커를 이용한 오이 유통품종 DNA Profile Data Base 구축)

  • Kwon, Yong-Sham;Choi, Keun-Jin
    • Horticultural Science & Technology
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    • v.31 no.3
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    • pp.344-351
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    • 2013
  • Microsatellite is one of the most suitable marker for cultivar identification as it has great discrimination power for cultivars with narrow genetic variation. The polymorphism level between 358 microsatellite primer pairs and 11 commercial cucumber cultivars was investigated. Thirty-one primer pairs showed high polymorphism within cucumber cultivars with different fruit types. These markers were applied for the constructing DNA profile data base of 110 commercial cucumber cultivars through multiplex PCR and fluorescence based automatic detection system. A total of 139 polymorphic amplified fragments were obtained by using 31 microsatellite markers. The average of PIC value was 0.610 ranging from 0.253 to 0.873. One hundred and thirty nine microsatellite loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of microsatellite analysis, were categorized into plant shape and fruit type. Almost the cultivars were discriminated by marker genotypes. This information may be useful to compare through genetic relationship analysis between existing variety and candidate varieties in distinctive tests and protection of plant breeders' intellectual property rights through variety identification.

Scoring Korean Written Responses Using English-Based Automated Computer Scoring Models and Machine Translation: A Case of Natural Selection Concept Test (영어기반 컴퓨터자동채점모델과 기계번역을 활용한 서술형 한국어 응답 채점 -자연선택개념평가 사례-)

  • Ha, Minsu
    • Journal of The Korean Association For Science Education
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    • v.36 no.3
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    • pp.389-397
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    • 2016
  • This study aims to test the efficacy of English-based automated computer scoring models and machine translation to score Korean college students' written responses on natural selection concept items. To this end, I collected 128 pre-service biology teachers' written responses on four-item instrument (total 512 written responses). The machine translation software (i.e., Google Translate) translated both original responses and spell-corrected responses. The presence/absence of five scientific ideas and three $na{\ddot{i}}ve$ ideas in both translated responses were judged by the automated computer scoring models (i.e., EvoGrader). The computer-scored results (4096 predictions) were compared with expert-scored results. The results illustrated that no significant differences in both average scores and statistical results using average scores was found between the computer-scored result and experts-scored result. The Pearson correlation coefficients of composite scores for each student between computer scoring and experts scoring were 0.848 for scientific ideas and 0.776 for $na{\ddot{i}}ve$ ideas. The inter-rater reliability indices (Cohen kappa) between computer scoring and experts scoring for linguistically simple concepts (e.g., variation, competition, and limited resources) were over 0.8. These findings reveal that the English-based automated computer scoring models and machine translation can be a promising method in scoring Korean college students' written responses on natural selection concept items.

Analysis of Vertical Profiles and Optical Characteristics of the Asian Dust Using Ground-based Measurements (지상관측장비를 이용하여 관측한 봄철 황사의 연직분포와 광학적 특성 분석)

  • Lee, Byung-Il;Yoon, Soon-Chang;Kim, Yoonjae
    • Atmosphere
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    • v.18 no.4
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    • pp.287-297
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    • 2008
  • The vertical profiles and optical properties of Asian dust are investigated using ground-based measurements from 1998 to 2002. Vertical profiles of aerosol extinction coefficient are evaluated using MPL (Micro Pulse Lidar) data. Optical parameters such as aerosol optical thickness ($\tau$), ${\AA}ngstr\ddot{o}m$ exponent ($\alpha$), single scattering albedo ($\omega$), refractive index, and volume size distribution are analyzed with sun/sky radiometer data for the same period. We can separate aerosol vertical profiles into three categories. First category named as 'Asian dust case', which aerosol extinction coefficient is larger than $0.15km^{-1}$ and dust layer exists from surface up to 3-4km. Second category named as 'Elevated aerosol case', which aerosol layer exists between 2 and 6km with 1-2.5km thickness, and extinction coefficient is smaller than $0.15km^{-1}$. Third category named as 'Clear sky case', which aerosol extinction coefficient appears smaller than $0.15km^{-1}$. and shows that diurnal variation of background aerosol in urban area. While optical parameters for first category indicate that $\tau$ and $\alpha$ are $0.63{\pm}0.14$, $0.48{\pm}0.19$, respectively. Also, aerosol volume concentration is increased for range of 1 and $4{\mu}m$, in coarse mode. Optical parameters for second category can be separated into two different types. Optical properties of first type are very close to Asian dust cases. Also, dust reports of source region and backward trajectory analyses assure that these type is much related with Asian dust event. However, optical properties of the other type are similar to those of urban aerosol. For clear sky case, $\tau$ is relatively smaller and $\alpha$ is larger compare with other cases. Each case shows distinct characteristics in aerosol optical parameters.

Single Laboratory Validation and Uncertainty Estimation of a HPLC Analysis Method for Deoxynivalenol in Noodles (면류에서 HPLC를 이용한 데옥시니발레놀 분석법의 검증과 불확도 산정)

  • Ee, Ok-Hyun;Chang, Hyun-Joo;Kang, Young-Woon;Kim, Mee-Hye;Chun, Hyang-Sook
    • Journal of Food Hygiene and Safety
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    • v.26 no.2
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    • pp.142-149
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    • 2011
  • An isocratic high performance liquid chromatography (HPLC) method for routine analysis of deoxynivalenol in noodles was validated and estimated the measurement uncertainty. Noodles (dried noodle and ramyeon) were analyzed by HPLC-ultraviolet detection using immunoaffinity column for clean-up. The limits of detection (LOD) and quantification (LOQ) were 7.5 ${\mu}g$/kg and 18.8 ${\mu}g$/kg, respectively. The calibration curve showed a good linearity, with correlation coefficients $r^2$ of 0.9999 in the concentration range from 20 to 500 ${\mu}g$/kg. Recoveries and Repeatabilities expressed as coefficients of variation (CV) spiked with 200 and 500 ${\mu}g$/kg were $82{\pm}2.7%$ and $87{\pm}1.3%$% in dried noodle, and $97{\pm}1.6%$ and $91{\pm}12.0%$ in ramyeon, respectively. The uncertainty sources in measurement process were identified as sample weight, final volume, and sample concentration in extraction volume as well as components such as standard stock solution, working standard solution, 5 standard solutions, calibration curve, matrix, and instrument. Deoxynivalenol concentration and expanded uncertainty in two matrixes spiked with 200 ${\mu}g$/kg and 500 ${\mu}g$/kg were estimated to be $163.8{\pm}52.1$ and $435.2{\pm}91.6\;{\mu}g$/kg for dried noodle, and $194.3{\pm}33.0$ and $453.2{\pm}91.1\;{\mu}g$/kg for ramyeon using a coverage factor of two which gives a level of statistical confidence with approximately 95%. The most influential component among uncertainty sources was the recovery of matrix, followed by calibration curve.

The Variation of Natural Population of Pinus densiflora S. et Z. in Korea (III) -Genetic Variation of the Progeny Originated from Mt. Chu-wang, An-Myon Island and Mt. O-Dae Populations- (소나무 천연집단(天然集團)의 변이(變異)에 관(關)한 연구(硏究)(III) -주왕산(周王山), 안면도(安眠島), 오대산(五臺山) 소나무집단(集團)의 차대(次代)의 유전변이(遺傳變異)-)

  • Yim, Kyong Bin;Kwon, Ki Won
    • Journal of Korean Society of Forest Science
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    • v.32 no.1
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    • pp.36-63
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    • 1976
  • The purpose of this study is to elucidate the genetic variation of the natural forest of Pinus densiflora. Three natural populations of the species, which are considered to be superior quality phenotypically, were selected. The locations and conditions of the populations are shown in table 1 and 2. The morphological traits of tree and needle and some other characteristics were presented already in our first report of this series in which population and family differences according to observed characteristics were statistically analyzed. Twenty trees were sampled from each populations, i.e., 60 trees in total. During the autumn of 1974, matured cones were collected from each tree and open-pollinated seeds were extracted in laboratory. Immediately after cone collection, in closed condition, the morphological characteristics were measured. Seed and seed-wing dimensions were also studied. In the spring of 1975, the seeds were sown in the experimental tree nursery located in Suweon. And in the April of 1976, the 1-0 seedlings were transplanted according to the predetermined experimental design, randomized block design with three replications. Because of cone setting condition. the number of family from which progenies were raised by populations were not equal. The numbers of family were 20 in population 1. 18 in population 2 and 15 in population 3. Then, each randomized block contained seedlings of 53 families from 3 populations. The present paper is mainly concerned with the variation of some characteristics of cone, seed, needle, growth performance of seedlings, and chlorophyll and monoterpene compositions of needles. The results obtained are summerized as follows. 1. The meteorological data obtained by averaging the records of 30 year period, observed from the nearest station to each location of populations, are shown in Fig. 3, 4, and 5. The distributional pattern of monthly precipitation are quite similar among locations. However, the precipitation density on population 2, Seosan area, during growing season is lower as compared to the other two populations. Population 1. Cheong-song area, and population 3, Pyong-chang area, are located in inland, but population 2 in the western seacoast. The differences on the average monthly air temperatures and the average monthly lowest temperatures among populations can hardly be found. 2. Available information on the each mother trees (families) studied, such as age, stem height, diameter at breast height, clear-bole-length, crown conditions and others are shown in table 6,7, and 8. 3. The measurements of fresh cone weight, length and the widest diameter of cone are given in Tab]e 9. All these traits arc concerned with the highly significant population differences and family differences within population. And the population difference was also found in the cone-index, that is, length-diameter ratio. 4. Seed-wing length and seed-wing width showed the population differences, and the family differences were also found in both characteristics. Not discussed in this paper, however, seed-wing colours and their shapes indicate the specificity which is inherent to individual trees as shown in photo 3 on page 50. The colour and shape are fully the expression of genetic make up of mother tree. The little variations on these traits are resulted from this reason. The significant differences among populations and among families were found in those characteristics, such as 1000-seed weight, seed length, seed width, and seed thickness as shown in table 11. As to all these dimensions, the values arc always larger in population 1 which is younger in age than that of the other two. The population differences evaluated by cone, seed and seed-wing sizes could partly be attributed to the growth vigorousity. 5. The values of correlation between the characteristics of cone and seed are presented in table 12. As shown, the positive correlations between cone diameter and seed-wing width were calculated in all populations studied. The correlation between seed-wing length and seed length was significantly positive in population 1 and 3 but not in population 2, that is, the r-value is so small as 0.002. in the latter. The correlation between cone length and seed-wing length was highly significant in population 1, but not in population 2. 6. Differences among progenies in growth performances, such as 1-0 and 1-1 seedling height and root collar diameter were highly singificant among populations as well as families within population(Table 13.) 7. The heritability values in narrow sense of population characteristics were estimated on the basis of variance components. The values based on seedling height at each age stage of 1-1 and 1-0 ranged from 0.146 to 0.288 and the values of root collar diameter from 0.060 to 0.130. (Table 14). These heritability values varied according to characteristics and seedling ages. Here what must be stated is that, for calculation of heritability values, the variance values of population was divided by the variance value of environment (error) and family and population. The present authors want to add the heritability values based on family level in the coming report. It might be considered that if the tree age is increased in furture, the heritability value is supposed to be altered or lowered. Examining the heritability values studied previously by many authors, in pine group at age of 7 to 15, the values of height growth ranged from 0.2 to 0.4 in general. The values we obtained are further below than these. 8. The correlation between seedling growth and seed characteristics were examined and the values resulted are shown in table 16. Contrary to our hypothetical premise of positive correlation between 1-0 seedling height and seed weight, non-significance on it was found. However, 1-0 seedling height correlated positively with seed length. And significant correlations between 1-0 and 1-1 seedling height are calculated. 9. The numbers of stomata row calculated separately by abaxial and adaxial side showed highly significant differences among populations, but not in serration density. On serration density, the differences among families within population were highly significant. (Table 17) A fact must be noted is that the correlation between stomata row on abaxial side and adaxial side was highly significant in all populations. Non-significances of correlation coefficient between progenies and parents regarding to stomata row on abaxial side were shown in all populations studied.(Table 18). 10. The contents of chhlorophyll b of the needle were a little more than that of chlorophyll a irrespective of the populations examined. The differences of chlorophyll a, b and a plus b contents were highly significant but not among families within populations as shown in table 20. The contents of chlorophyll a and b are presented by individual trees of each populations in table 21. 11. The occurrence of monoterpene components was examined by gas liquid chromatography (Shimazu, GC-1C type) to evaluate the population difference. There are some papers reporting the chemical geography of pines basing upon monoterpene composition. The number of populations studied here is not enough to state this problem. The kinds of monoterpene observed in needle were ${\alpha}$-pinene, camphene, ${\beta}$-pinene, myrcene, limonene, ${\beta}$-phellandrene and terpinolene plus two unknowns. In analysis of monoterpene composition, the number of sample trees varied with population, I.e., 18 families for population 1, 15 for population 2 and 11 for population3. (Table 22, 23 and 24). The histograms(Fig. 6) of 7 components of monoterpene by population show noticeably higher percentages of ${\alpha}$-pinene irrespective of population and ${\beta}$-phellandrene in the next order. The minor Pinus densiflora monoterpene composition of camphene, myrcene, limonene and terpinolene made up less than 10 percent of the portion in general. The average coefficients of variation of ${\alpha}$-pinene and ${\beta}$-phellandrene were 11 percent. On the contrary to this, the average coefficients of variation of camphene, limonene and terpinolene varied from 20 to 30 percent. And the significant differences between populaiton were observed only in myrcene and ${\beta}$-phellandrene. (Table 25).

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