• Plant Resources
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• v.7 no.1
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• pp.65-68
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• 2004

We used an amplified fragment length polymorphism (AFLP) analysis, a novel PCR-based technique, to differentiate Xanthomonas oryzae pv. oryzae (Xoo) of Korean races. The 6 strains of Xoo K1, K2, K3 races were tested with 81 AFLP primer combinations to identify the best selective primers. The primer combinations were selected according to their reproducibility, number of polymorphic bands and polymorphism detected among Xoo strains. 18 strains of Xoo K1, K2 and K3 races were analyzed with the selected combinations of primer set. Some primer combinations (Eco R I +1 / Mse I+1) could differentiate Xoo of Korean races that were not distinguished by other fingerprinting analysis. Thus AFLP fingerprinting permitted very fine discrimination among different races.

• Korean Journal of Veterinary Research
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• v.41 no.2
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• pp.157-165
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• 2001

Amplified fragment length polymorphism(AFLP) technique is based on the polymorphism detection through selective PCR amplification of restriction fragments from digested genomic DNA and thus includes the procedures of the total DNA digestion by endonucleases, ligation of adapters to the ends of the fragments, and following the selective amplification of the restricted DNA fragments. This study were aimed to : (1) determine the genetic variability of S aureus strains, (2) estimate genetic diversity within and among these strains, (3) compare phylogenetic relationships among these strains as genetic markers using AFLP techniques. Genomic DNA was digested with a particular combination of three restriction enzymes with specific recognition sites and the DNA fragments were ligated to restriction specific adapters and amplified using the selective primer combinations. In the S aureus strain, the number of scorable AFLP bands detected per each primer combination varied from 29 to 102, with an average of 61.59 using 27 primer combinations. A total of 1,663 markers were generated, 904 bands of which were polymorphic, showing a 33.48% level of polymorphism with these primer combinations. Among the primer combinations, E02/T02, E02/T03, E04/H02, E02/T01 and E04/H03 primer combinations showed a high level of polymorphism with 0.78, 0.76, 0.74, 0.71 and 0.70, respectively. But T03/H01, E01/T02 and E01/T03 primer combinations showed a low level of polymorphism with 0.38, 0.37 and 0.15, respectively, Therefore, the former primer combinations will be the most effective for AFLP analysis of S aureus. In SA1 sub-types the level of polymorphism of S aureus KCTC 1927 was similar to that of S aureus CU 01(0.825) and higher than those of other strains such as S aureus CU 02 (0.715), S aureus KCTC 2199(0.625), S aureus KCTC 1916(0.607) and S aureus KCTC 1621 (0.553). In SA2 sub-types the level of polymorphism of S aureus CU 07 was similar to that of S aureus CU 08(0.935) and higher than those of both S aureus CU 04(0.883) and S aureus CU 05(0.883) and lower than those of S aureus CU 03(0.583). In SA3 subtypes the level of polymorphism of S aureus CU 11 was similar to that of S aureus CU 12(0.913) and lower than that of S aureus CU 15(0.623). The results proved that AFLP marker analysis of S aureus strain could be used to study the epidemiology of mastitis and in addition, common genotype in geographic region could be useful for the development of an effective vaccine or DNA marker for easy diagnosis of mastitis caused by S aureus infection.

• Research in Plant Disease
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• v.24 no.4
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• pp.348-352
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• 2018

A multiplex reverse transcription-polymerase chain reaction (mRT-PCR) assay was developed for the detection of Clover yellow vein virus (ClYVV), Peanut mottle virus (PeMoV), and Tomato spotted wilt virus (TSWV), which were recently reported to infect soybean and azuki bean in Korea. Species-specific primer sets were designed for the detection of each virus, and their specificity and sensitivity were tested using mixed primer sets. From among the designed primer sets, two combinations were selected and further evaluated to estimate the detection limits of uniplex, duplex, and multiplex RT-PCR. The multiplex RT-PCR assay could be a useful tool for the field survey of plant viruses and the rapid detection of ClYVV, PeMoV, and TSWV in leguminous plants.

• Plant Resources
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• v.5 no.3
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• pp.169-175
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• 2002

The soybean cyst nematode (Heterodera glycines Inchinoe; SCN) is a devastating pest of soybean and is responsible for significant losses in yield. The use of resistant cultivars is the effective method to reduce or eliminate SCN damage. The objective of this research is to identify AFLP markers linked to the SCN resistant genes. Bulked genomic DNA was made from resistant and susceptible genotypes to SCN and a total of 19 primer combinations were used. About 31 fragments were detected per primer combination. The banding patterns were readily distinguished in resistant and susceptible bulked genotypes. Polymorphic fragments were detected between resistant and susceptible bulked genotypes in the primer combination of CGT/GGC, CAG/GTG and CTC/GAG. In primer combinations of CGT/GGC and CAG/GTG, bulked resistant genotype produced a polymorphic bands. However, in primer of CTC/GAG, bulked susceptible genotype produced a polymorphic fragments. Three AFLP markers identified as a polymorphic fragments between bulked genomic DNA were mapped in 85 F2 population. Among them, only two markers, CGT/GGC and CTC/GAG, was linked and was mapped. Broad application of AFLP marker would be possible for improving resistant cultivars to SCN.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.4
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• pp.358-362
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• 2004

In order to develop molecular markers related to stay green phenotype, AFLP analysis was conducted using near-isogenic lines for either stay green or non stay green trait. Both lines have characteristics of multi-ear and tillers (MET). Two out of 64 primer combinations of selective amplification identified three reproducible polymorphic fragments in MET corn with stay green. Both of E+AGC/M+CAC and E+AAG/M+CAA primer combinations produced two and one specific polymorphic fragments linked to stay green trait, respectively. For the conversion of AFLPs to sequence tag sites (STSs), primers were designed form both end sequences of each two polymorphic fragments. One fragment, which was amplified with E+AAG/M+CAA primer combinations, possessed 298 bp long and showed a $91\%$ homology with maize retrotransposon Cinful-l. One out of two polymorphic fragments produced with E+AGC/M+CAC primer combination had 236 bp long and matched a $96\%$ homology with an intron region of 22kDa alpha zein gene cluster in Zea mays. One out of two PCR fragments amplified with MET2 primer set in the stay green MET was not produced in the non-stay green MET. The developed AFLP and STS marker could be used as an efficient tool for selection of the stay green trait in the MET inbred.

• Food Science of Animal Resources
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• v.22 no.4
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• pp.301-309
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• 2002

This study was carried out to develop the breed-specific DNA markers for breed identification of Korean native goat meat using amplified fragment length polymorphism (AFLP)-PCR techniques. The genomic DNAs of Korean native goat, imported black goat and four dairy goat breeds(Saanen, Alpine, Nubian and Toggenburg) were extracted from muscle tissues or blood. Genomic DNA was digested with a particular combination of two restriction enzymes with 4 base(Mse I and Taq I) and 6 base(EcoR I and Hind III) recognition sites, ligated to restriction specific adapters and amplified using the selective primer combinations. In AFLP profiles of polyacrylamide gels, the number of scorable bands produced per primer combination varied from 36 to 74, with an average of 55.5. A total of 555 bands were produced, 149(26.8%) bands of which were polymorphic. Among the ten primer combinations, two bands with 2.01 and 1.26 kb in M13/H13 primer and one band with 1.65 kb in E35/H14 primer were found to be breed-specific AFLP markers in Korean native goat when DNA bands were compared among the goat breeds. In the E35/H14 primer combination, 2.19, 2.03, 0.96 and 0.87 kb bands detected in imported black goat, 2.13 kb band in Saanen breed and 2.08 kb band in Nubian breed were observed as breed-specific bands showing differences between goat breeds, respectively. The E35/H14 primer combination produced four DNA bands distinguished between Korean native goat and Saanen breed. The is study suggested that the breed specific AFLP bands could be used as DNA markers for the identification of Korean native goat meat from imported black goat and dairy goat meats.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2001.05a
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• pp.559-560
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• 2001

The objective of the present study was to analyze genetic variation and characteristics in rainbow trout(Oncorhynchus mykiss) using amplified fragment length polymorphism(AFLP) method as molecular genetic technique, to evaluate the usefulness of AFLP as genetic markers, and to compared the efficiency of agarose and polyacrylamide sequencing gels. The amplified products were performed by agarose and sequencing gel electrophoresis to detect AFLP band patterns, respectively. Using 9 primer combinations, total of 141 AFLP bands were produced, 108 bands(82.4％) of which were polymorphic in agarose gels. In sequencing gels, total of 288 bands were generated, and 220 bands (76.4％) were polymorphic. The level of bandsharing(BS) ranged from 0.18 to 0.32 for the 9 primer combinations tested, with a mean of 0.24. Consequently, AFLP markers of these rainbow trout 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 importment traits in fish species.

• Journal of Radiation Industry
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• v.6 no.1
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• pp.23-29
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• 2012

In this study, we investigated the genetic variation in the general of monocot model plant (rice) in response to various ionizing irradiations including gamma-ray, ion beam and cosmic-ray. The non-irradiated and three irradiated (200 Gy of gamma-ray and 40 Gy of ion beam and cosmic-ray) plants were analyzed by AFLP technique using capillary electrophoresis with ABI3130xl genetic analyzer. The 29 primer combinations tested produced polymorphism results showing a total of 2,238 bands with fragments sizes ranged from 30 bp to 600 bp. The number of polymorphism generated by each primer combinations was varied significantly, ranging from 2 (M-CAC/E-ACG) to 158 (M-CAT/E-AGG) with an average of 77 bands. Polymorphic peaks were detected as 1,269 with an average of 44 per primer combinations. By UPGMA (Unweighted Pair Group Method using Arithmetic clustering) analysis method, the clusters were divided into non-irradiated sample and three irradiated samples at a similarity coefficient of 0.41 and three irradiation samples was subdivided into cosmic-ray and two irradiation samples (200 Gy of gamma-ray and 40 Gy of ion beam) at similarity coefficient of 0.48. Similarity coefficient values ranged from 0.41 to 0.55.

• Plant Breeding and Biotechnology
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• v.2 no.3
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• pp.224-230
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• 2014

Amplified fragment length polymorphism (AFLP) is a molecular marker technique based on DNA and is extremely useful in detection of high polymorphism between closely related genotypes like Korean wheat cultivars. Six sequence characterized amplified regions (SCARs) have been developed from inter simple sequence repeat (ISSR) analysis which enabled the identification and differentiation of 13 Korean wheat cultivars from the other cultivars. We used six combinations of primer sets in our AFLP analysis for developing additional cultivar-specific markers in Korean wheat. Fifty-eight of the AFLP bands were isolated from EA-ACG/MA-CAC, EA-AGC/MA-CTG and EA-AGG/MA-CTA primer combinations. Of which 40 bands were selected to design SCAR primer pairs for Korean wheat cultivar identification. Three of 58 amplified primer pairs, KWSM006, KWSM007 and JkSP, enabled wheat cultivar identification. Consequently, 23 of 32 Korean wheat cultivars were classified by eight SCAR marker sets.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.42 no.2
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• pp.146-150
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• 2009

Genetic variation and relationship of two wild (Pampus argenteus and P. echinogaster) and one cultured (P. chinesis) pomfret fish belonging to the genus Pampus were assessed. Specimens were collected from Korea and China and subjected to amplified fragment length polymorphism (AFLP) DNA fingerprinting. Four primer combinations generated a total of 304 DNA fragments ranging from 153 to 251 bands. Polymorphism and genetic diversity of cultured P. chinensis (22.9% and 0.038) were significantly lower than the two wild species of P. argenteus (93.6% and 0.311) and P. echinogaster (94.0% and 0.290). Genetic distance ranged from 0.335 (P. argenteus and P. echinogaster) to 0.646 (P. argenteus and P. chinensis) and showed a congeneric relationship within this genus. Twenty one of specific AFLP markers from four primer combinations bands were produced. These results suggest that AFLP polymorphism may be a useful marker for genetic identification among the three species studies here.