• The Plant Pathology Journal
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• v.30 no.4
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• pp.425-431
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• 2014

Leaf scald caused by the infection of Rhynchosporium secalis, is a worldwide crop disease resulting in significant loss of barley yield. In this study, a systematic sequencing of expressed sequence tags (ESTs) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant ESTs, which are induced at different time points, an amplified fragment length polymorphism (AFLP) display of complementary DNA (cDNA) was utilized. Transcriptional changes of 140 ESTs were observed, of which 19 have no previously described function. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding classical pathogenesis-related (PR) or genes that play a role in the signal transduction pathway. The expression analyses by a semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) revealed that Rar1 and Rpg4 are defense inducible genes, and were consistent with the cDNA-AFLP data in their expression patterns. Hence, the here presented transcriptomic approach provides novel global catalogue of genes not currently represented in the EST databases.

• Mycobiology
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• v.31 no.4
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• pp.229-234
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• 2003

A total of 24 isolates of Phytophthora infestans were tested and analyzed for their resistance to metalaxyl fungicides. Sensitivity to metalaxyl was determined by growing isolates on 20% V8 medium amended with 0, 5, and 100 ${\mu}g/ml$ metalaxyl. Four isolates among the 24 tested were resistant to metalaxyl. Eleven isolates were intermediate and nine isolates were sensitive. Amplified fragment length polymorphism(AFLP) assay was used to identify the amplification products of resistant isolates. As a result, selected fragments were cloned, sequences and primer pairs were developed which linked to metalaxyl insensitivity in P. infestans using competitive PCR.

• Journal of Plant Biotechnology
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• v.7 no.2
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• pp.81-86
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• 2005

Panax ginseng is one of the most important medicinal plants in the world. The international trade of ginseng is increasing yearly. The disguise of Chinese and American ginseng into Korean ginseng became a problem in recent years in abroad and Korea. An effective method to authenticate the Korean Panax ginseng from others at a DNA level is necessary for the healthy development of the ginseng market. Amplified fragment length polymorphism (AFLP) analysis was applied to develop a method for the identification of Korean ginseng between Chinese ginseng and American ginseng. It is very difficult to detect the different polymorphic bands among Korean field cultivated ginseng, and between field and wild-cultivated ginseng. The genetic distance coefficient by AFLP analysis between field- and wild cultivated Korean ginseng was very low, 0.056. Whereas, polymorphic bands between Korean and Chinese wild-cultivated ginseng was significantly different. The genetic distance coefficient between wild-cultivated Korean and Chinese ginseng was 0.149. The genetic distance coefficients between the P. ginseng and P. quinquefolius were ranging from 0.626 to 0.666. These results support that the AFLP analysis could be applied to authenticate Korean P. ginseng from others Chinese P. ginseng and American ginseng (P. quinquefolius).

• Korean Journal of Fisheries and Aquatic Sciences
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• v.41 no.2
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• pp.94-101
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• 2008

In Korean waters, there are two color types (blue and purple) of the blue crab Portunus trituberculatus. The blue type is common, but the ratio of the purple type has increased in landings. To determine whether there were significant morphometric or genetic differences between the blue and purple types, crabs caught from the West Sea of Korea were examined. Based on covariance analysis, there were significant differences in 1 of 10 morphometric characteristics of males between the two types, in none of the ten characteristics for females. Using amplified fragment length polymorphism (AFLP) DNA fingerprinting, no specific AFLP marker was detected for each type. The heterozygosity and genetic diversity were very low. Analyses of pairwise distance, the Fst index, and genetic similarity revealed similar results, with very low genetic differentiation. Therefore, there is no significant difference between blue and purple types of the crab from the West Sea of Korea, and the two types in the West Sea can be managed as one stock.

• Journal of Ecology and Environment
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• v.29 no.6
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• pp.503-509
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• 2006

To determine the minimum area for conservation of four Halophytic species populations, we evaluate the genetic diversity of four species based on the AFLP method using thirteen primer sets. Four species populations, Phragmites communis Trin, Suaeda japonica Makino, Zoysia sinica Hance, and S. maritima (L.) Dumort, from the southwestern coast of Korea, were selected for this study. The genetic diversity index ($\Psi_{ST}$) of Phragmites communis was 0.3856, Suaeda japonica 0.1445, Suaeda maritima 0.1669, and Zoysia sinica 0.2422. Based on the genetic diversity of population, we could determine the minimum area for conservation of each species as follows. P. communis needs $500{\times}500m^2$, S. japonica, S. maritima, and Z. sinica $100\times100m^2$ for keeping their genetic identity.

• Journal of Aquaculture
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• v.17 no.1
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• pp.69-80
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• 2004

The objective of the present study was to analyze genetic distances, variation and characteristics of individuals in rainbow trout, Oncorhynchus mykis using amplified fragment length polymorphism (AFLP) method as molecular genetic technique, to detect AFLP band patterns as genetic markers, and to compare the efficiency of agarosegel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively. Using 9 primer combinations, a total of 141 AFLP bands were produced, 108 bands (82.4%) of which were polymorphic in AGE. In PAGE, a total of 288 bands were detected, and 220 bands (76.4%) were polymorphic. The AFLP fingerprints of AGE were different from those of PAGE. Separation of the fragments with low molecular weight and genetic polymorphisms revealed a distinct pattern in the two gel systems. In the present study, the average bandsharing values of the individuals between two populations apart from the geographic sites in Kangwon-do ranged from 0.084 to 0.738 of AGE and PAGE. The bandsharing values between individuals No.9 and No. 10 showed the highest level within population, whereas the bandsharing values between individuals No.5 and No.7 showed the lowest level. As calculated by bandsharing analysis, an average of genetic difference (mean$\pm$SD) of individuals was approximately 0.590$\pm$0.125 in this population. In AGE, the single linkage dendrogram resulted from two primers (M11+H11 and M13+H11), indicating six genetic groupings composed of group 1 (No.9 and 10), group 2 (No. 1, 4, 5, 7, 10, 11, 16 and 17), group 3 (No. 2, 3, 6, 8, 12, 15 and 16), group 4 (No.9, 14 and 17), group 5 (No. 13, 19, 20 and 21) and group 6 (No. 23). In AGE, the genetic distances among individuals of between-population ranged from 0.108 to 0.392. In AGE, the shortest genetic distance (0.108) displaying significant molecular differences was between individuals No.9 and No. 10. Especially, the genetic distance between individuals No. 23 and the remnants among individuals within population was highest (0.392). Additionally, in the cluster analysis using the PAGE data, the single linkage dendrogram resulted from two primers (M12+H13 and M11+H13), indicating seven genetic groupings composed of group 1 (No. 15), group 2 (No. 14), group 3 (No. 11 and 12), group 4 (No.5, 6, 7, 8, 10 and 13), group 5 (No.1, 2, 3 and 4), group 6 (No.9) and group 7 (No. 16). By comparison with the individuals in PAGE, genetic distance between No. 10 and No. 7 showed the shortest value (0.071), also between No. 16 and No. 14 showed the highest value (0.242). As with the PAGE analysis, genetic differences were certainly apparent with 13 of 16 individuals showing greater than 80% AFLP-based similarity to their closest neighbor. The three individuals (No. 14, No. 15 and No. 16) of rainbow trout between two populations apart from the geographic sites in Kangwon-do formed distinct genetic distances as compared with other individuals. These results indicated that AFLP markers of this fish could be used as genetic information such as species identification, genetic relationship or analysis of genome structure, and selection aids for genetic improvement of economically important traits in fish species.

• Korean Journal of Plant Resources
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• v.27 no.3
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• pp.249-255
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• 2014

The rice belonging to Oryza sativa is not only has significant economic importance, for it is the major source of nutrition for about 3 billion all around the world. But also plays a vital role as a model organism, because it has a number of advantages to be a model plant, such as efficient transformation system and small genome size. Many methods and techniques have been conducted to attempt to distinguish different Oryza sativa species, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and so on. However, studies using sequence analysis of internal transcribed spacer (ITS), a region of ribosomal RNA has not been reported until now. This study was undertaken with an aim to understand the phylogenetic relationships among sixteen isolates of Oryza sativa collected from abroad and fifteen isolates collected from Korea, using ribosomal RNA (rRNA) internal transcribed spacer (ITS) sequences to compare the phylogeny relationships among different Oryza sativa species. The size variation obtained among sequenced nuclear ribosomal DNA (nrDNA) ITS region ranged from 515bp to 1000bp. The highest interspecific genetic distance (GD) was found between Sfejare 45 (FR12) and Anapuruna (FR15). Taebong isolate showed the least dissimilarity of the ITS region sequence with other thirty isolates. This consequence will help us further understanding molecular diversification in intra-species population and their phylogenetic analysis.

• Korean Journal of Plant Taxonomy
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• v.39 no.2
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• pp.63-73
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• 2009

$Iso{\ddot{e}}tes$ L. ($Iso{\ddot{e}}taceae$) is difficult to identify among the infrageneric taxa because of morphological simplicity. Since two species (I. japonica and I. coreana) had been reported, I. jejuensis and I. hallasanensis were described as two new species from Jeju Island, South Korea. The habitats of all species were confirmed by current studies except for I. japonica. We compared the morphological and anatomical characters of seven species, three domestic species and four species in adjacent regions (I. taiwanensis, I. sinensis, I. japonica, and I. asiatica). I. asiatica differs from other species in the lobe number of corm, spreading sporophylls, lack of stomata and degree of velum development. All of the seven species were identified by the characteristics of their mega- and microspores. Especially, it was possible to identify the four species in South Korea by the types of ornamentation on their megaspores. Each species has a specific type of megaspore ornamentation: I. coreana - cristate, I. jejuensis - rugulate, I. hallasanensis - echinate, and I. japonica - reticulate. We also discussed the phylogeny of the genus in East Asia in relation to recent studies based on the second intron of LEAFY sequence and amplified fragment length polymorphism (AFLP) analysis. We suggest strategies for the conservation of the endangered $Iso{\ddot{e}}tes$ species in South Korea.

• The Korean Journal of Mycology
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• v.41 no.1
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• pp.14-20
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• 2013

We already reported four groups which contains some similar strains based on URP-PCR in the previous paper. The objective of this study was to confirm those strains by the amplified fragment length polymorphism (AFLP) and vegetative compatibility group (VCG). AFLP analysis showed no difference among these strains except ASI 2595 and 2183 in Weonhyeong group and ASI 2829 in Suhan group. They showed specific DNA bands only in the result of P + AG/M + AAG and P + GT/M + ATG primer combinations out of eight different combinations. The AFLP primers produced a total of 330 fragments between 80 and 1000 bp in length for 31 Pleurotus ostreatus strains. At a genetic similarity of 0.96, the UPGMA analysis separated the isolates into four distinct clusters. Each group was classified by similar strains. Confrontation test by vegetative compatibility groups (VCGs) also showed distinct line between strains from different groups, but no line between similar strains within the cluster. Our results indicate that most of similar strains was not distinctness. Thus, similar strains are considered to be very close on the genealogy of their parent or same strain with different name.

• Korean Journal of Environmental Biology
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• v.34 no.3
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• pp.169-176
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• 2016

Although chemical fertilizers have a quick effect and broad applicability to agricultural fields, they have caused many problems like increasing soil acidity or decreasing soil organic matters. Environmental-friendly agriculture has been attempted in various ways such as organic agriculture, natural farming, low input and sustainable agriculture. The common interest of all environmental-friendly systems is to decrease burden to agricultural environment by low input of agricultural labor and materials. This study was conducted to estimate overwintering capacity and genetic distance among Chinese Milk Vetch (Astragalus sinicus, CMV) collections based on morphological characteristics and AFLP (Amplified fragment length polymorphism) analysis. Furthermore, the effect of CMV as green manure was observed in mix-cultured paddy fields with rice, sesame and sweet-potato. An another objective of this study was also to compare the pattern of weed occurrence in paddy fields with or without CMV and different rice transplanting times. The CMV collected from Paju district in central region of Korea was successively occurring through self-reseeding without artificial management. However, there was no noticeable difference in growth habit between Paju native CMV and introduced CMV from China which is currently used in farm fields. On the basis of multi-dimensional scaling and tree analyses, there are no significant difference of agricultural growth characteristics among Paju and chinese collections only excepting leaf angle and root length. The flowering time of Gurye collection was fast for 1 week as compared to other collections. AFLP that was commonly used for plant classfication, was applied to exam the genetic variation of CMV collections. Total 579 PCR products and 336 polymorphic fragments were generated using 8 primer pairs.