• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.5
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• pp.429-433
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• 2004

A single recessive gene, rxp, controls the bacterial leaf pustule (BLP) resistance in soybean and in our previous article, it has been mapped on linkage group (LG) D2 of molecular genetic map of soybean. A total of 130 recombinant inbred lines (RILs) from a cross between BLP-resistant SS2-2 and BLP-susceptible Jangyeobkong were used to identify molecular markers linked to rxp. Fifteen simple sequence repeat (SSR) markers on LG D2 were screened to construct a genetic map of rxp locus. Only four SSR markers, Satt135, Satt372, Satt448, and Satt486, showed parental polymorphisms. Using these markers, genetic scaffold map was constructed covering 26.2cM. Based on the single analysis of variance, Satt372 among these four SSR markers was the most significantly associated with the resistance to BLP. To develop new amplified fragment length polymorphism (AFLP) marker linked to the resistance gene, bulked segregant analysis (BSA) was employed. Resistance and susceptible bulks were made by pooling equal amount of genomic DNAs from ten of each in the segregating population. A total of 192 primer combinations were used to identify specific bands to the resistance, selecting three putative AFLP markers. These AFLP markers produced the fragment present in SS2-2 and the resistant bulk, and not in Jangyeobkong and the susceptible bulk. Linkage analysis revealed that McctEact97 $(P=0.0004,\;R^2=14.67\%)$ was more significant than Satt372, previously reported as the most closely linked marker.

• Korean Journal of Plant Resources
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• v.17 no.3
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• pp.265-271
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• 2004

Genetic variation is the basis of crop improvement. Limited genetic diversity in a crop species may restrict the amount of genetic improvement that can be achieved through plant breeding. Soybean is one of the world's most important crops. A potential source of genetic variability for the cultivated soybean is the wild species G. soja Sieb. ＆amp; Zucc. Amplified fragment length polymorphism (AFLP) analysis is a PCR-based technique, which can detect a 10-fold greater nubmer of loci than other DNA marker analysis. Twenty cultivated soybeans and two-hundred wild soybeans were used to determine genetic vatiations by AFLPs and evaluate the usefulness of AFLPs as DNA markers. Six-hundred and ten fragments were detected with an average of 56 AFLP fragments produced per primer in a total of 11 AFLP primer pairs. The number of polymorphic loci detected per primer ranged from 7 to 20 and the polymorphism was greater in wild than in cultivated soybean. F$_2$ segregation analysis of four AFLP fragments in combination of Hwaeomputkong ${\times}$ PI 417479 indicated that they segregate as stable Mendelian loci with 3 : 1. This results strongly suggest that the AFLP analysis is a good technique for the detection of genetic polymorphism in a wide plant species.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Journal of Korean Society of Forest Science
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• v.96 no.2
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• pp.125-130
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• 2007

The principal morphological characters used for identification of hydrangea cultivars are often dependent on agroclimatic conditions. Furthermore, information on the selection or the genetic background of the hydrangea breeding is so rare that a molecular marker system for cultivar identification is needed. Amplified fragment length polymorphism (AFLP) markers were employed for fingerprinting Hydrangea macrophylla cultivars and candidate cultivars of H. macrophylla selected in Korea. One AFLP primer combination was sufficient to distinguish 17 H. macrophylla cultivars and 4 candidate cultivars. The profile of 19 loci that can minimize the error of amplification peak detection was constructed. AFLP markers were efficient for identification, estimation of genetic distances between cultivars, and cultivar discrimination. Based on the observed AFLP markers, genetic relationship was reconstructed by the UPGMA method. Seventeen H. macrophylla cultivars and H. macrophylla for. normalis formed a major cluster, and candidate cultivars selected in Korea formed another cluster.

• Journal of the Korean Society of Tobacco Science
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• v.28 no.2
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• pp.94-99
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• 2006

AFLP(Amplified Fragment Length Polymorphism) analysis was conducted to cultivars of tobacco, Nicotiana tabacum in order to select the cultivar-specific markers. AFLP results using 12 primer sets revealed genetic diversity among 12 field grown tobacco cultivars. Polymorphic fragments amplified by PCR was purified and cloned to identify their nucleotide sequences. From the sequences of them, 40 primer sets were designed to select cultivar-specific markers. When genomic DNA isolated from tobacco were used as PCR template, a set of primers, BrSF/BrSR showed Burley-specific band patterns. The results indicate that AFLP technique used in this experiments is useful for identifying tobacco cultivars in a rapid manner.

• Korean Journal of Medicinal Crop Science
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• v.21 no.6
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• pp.455-460
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• 2013

Collected germplasms of five representative species belonging to Curcuma genus (C. longa, C. aromatica, C. zedoaria, C. phaeocaulis and C. kwangsiensis) were 52 samples from different farmhouse in Korea and China. To elucidate the genetic diversity among the species, 52 samples were analyzed by genomic fingerprinting method using amplified fragment length polymorphism (AFLP). AFLP results of 6 primer combinations were revealed 643 total DNA fragments and 349 polymorphic bands with the 54.3% ratio of polymorphism. In the analysis of coefficient similarity using unweight pair group method with arithmetic averages (UPGMA), 52 Curcuma germplasm lines were ranged from 0.60 to 0.99 and clustered distinct five groups according to the species and collected geographical levels. However, the result of principal coordinate analysis (PCA) by multi-variate analysis was shown significantly greater differences among species than geographical origins based on AFLP profiling data of these samples.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.9
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• pp.1241-1247
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• 2009

A large number of branded chicken products exist in Japan, and in some cases, the breed of chicken is an important factor used to attract consumer interest in the retail product. In order to establish a simple method for verifying such breed claims we applied the amplified fragment length polymorphism (AFLP) technique to nine chicken breeds (White Cornish, Red Cornish, White Plymouth Rock, New Hampshire, Rhode Island Red, Barred Plymouth Rock, Hinaidori, Tosajidori, Tsushimajidori) to search for molecular markers able to discriminate chicken breeds. Three breed-specific single nucleotide polymorphisms (SNP) were identified, one for each of Hinaidori, Tosajidori, or New Hampshire. A total of 219 individuals from the nine breeds were analyzed using a specific PCR test for each of these SNP. The PCR tests made it possible to discriminate between the breeds of chickens to identify products from these three breeds. This PCR method provides an efficient method for the routine analysis and verification of certified chicken products.

• Animal cells and systems
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• v.14 no.1
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• pp.31-36
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• 2010

The pinewood nematode Bursaphelenchus xylophilus causes pine wilt disease and is a serious economic concern for the forest industry of South Korea. To achieve effective control with limited resources, it is necessary to clarify the transmission routes and mechanisms of dispersal of this organism. Highly polymorphic and easy-to-use molecular markers can be used for investigating this aspect. In this study, we evaluated the usefulness of amplified fragment length polymorphisms (AFLPs) for investigating the genetic variations of B. xylophilus and related individuals from China, Japan, and South Korea. The AFLP patterns obtained in our study were similar to the microsatellite patterns reported in a previous study; our AFLP patterns indicated high genetic variability and cryptic genetic structure, but did not indicate any peculiar geographic structure. Moreover, the genetic distances between individuals suggested that the Korean population was affected to a greater extent by the Chinese population than the Japanese population. Further, the gene flow among the related species appeared to be limited; however, there may be also the possibility of genetic introgression among species. These results confirm the usefulness of AFLPs for understanding the epidemiology of pine wilt disease, thereby contributing to the effective control of this disease.

• Journal of Plant Biotechnology
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• v.4 no.4
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• pp.163-170
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• 2002

Radiation induced and somaclonal variations were investigated in the regenerates from gamma irradiated and controlled embryogenic callus (EC) of sweetpotato cvs., Yulmi and White Star by morphological, RAPD and AFLP analysis. Most (approx. 90%) of the EC produced somatic embryos developed into plantlets after being transferred to the auxin-free medium. The frequency of morphological variants derived from the irradiated callus ranged from 3 to 7.8% compared to 0.1-1.1% of that derived from the non-irradiated. Morphological variants were selected from the regenerates and analyzed by RAPD and AFLP procedures. RAPD polymorphisms of Yulmi and White Star regenerates from irradiated calli were 8.8% and 6.1%, respectively. However, the polymerphisms among regenerates from the non-irradiation treatment in these two cultivars were non-detectable and 3%, respectively. AFLP polymorphisms of Yulmi and White Star regenerates from irradiated calli were 29.9% and 28.6%, respectively. while the frequencies for those form non-irradiated calli were 8.5% and 5.6%, respectively. Both the control plants and variants from the nonirradiated were clustered together, while variants from irradiated were separated from the group by Nearest-Neighbor-Interchange Branch Swapping Abbreviation: EC (Embryogenic callus), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random amplified polymorphic DNA)

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.