• Journal of Animal Science and Technology
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• v.57 no.2
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• pp.5.1-5.8
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• 2015

Background: Korean native chicken (KNC) is a well-known breed due to its superior meat taste. This breed, however, owing to a low growth rate, has a high market price. In order to overcome this disadvantage, the National Institute of Animal Science (NIAS) in Korea developed a commercial KNC breed, named Woorimatdag version 2 (WM2), an upgraded version of the Woorimatdag (WM1) breed and the WM2 was created by crossing the KNC with meat type breeds. This study aims to discriminate between WM2 and other chicken breeds using microsatellite (MS) markers. Methods: A total of 302 individuals from eight Korean chicken populations were examined. The genetic diversity and population structure analysis were investigated using Cervus, API-CALC, STRUCTURE, PowerMarker programs. Results: Based on heterozygosity and polymorphic information content (PIC) values, 30 MS markers were initially selected from 150 markers. The identified average number of alleles (Na), expected heterozygosity, and PIC values for the WM2 samples were 7.17, 0.741, and 0.682, respectively. Additionally, the paternity of individuals was assigned with a success rate of greater than 99% using 12 markers, the best minimum number of markers. The 12 selected markers contained heterozygosity and PIC values above 0.7 and probability of identity values around zero. Using these markers, the determined probability of identity (PI), $PI_{half-sibs}$, and $PI_{sibs}$ values were 3.23E-33, 5.03E-22, and 8.61E-08, respectively. Conclusions: WM2 is well differentiated with respect to other chicken breeds based on estimated genetic distances. The results presented here will contribute to the identification of commercial WM2 chicken in the market.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.33-48
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• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.29 no.2
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• pp.136-151
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• 1984

The purpose of this study is to find out the linkage relationship of the resistance genes Wbph1 and Wbph2 which are known to be present in the rice cultivar N22 and ARC 10239 respectively, with the genetic markers which are identified as the specific linkage tester. Crosses were made between the resistant parents and the genetic marker stocks and their F$_2$ populations were grown out in the field. The genetic segregations of the marker character were studied and the seeds were harvested individual plant base. These F$_3$ seeds were grown into plant-line base in the greenhouse and their responses to the whitebacked planthopper were tested. Then the linkage relationship between the F$_2$ plant marker character and the F$_3$ resistance responses to the whitebacked planthopper were examined. In the F$_2$ generation of the crosses between the resistant parent N22 and the genetic marker stocks, the genetic markers, such as lg, d-t, g, la, bl and gl, showed the segregation of 3 dominance to 1 recessiveness, and the Bh marker segregated into 9:7 ratio. Another 4 marker genes, such as Cl, gh, Lh and bc, did not show the good fittness to the expected value. In the F$_2$ generation of the crosses between the resistant parent ARC 10239 and the genetic marker stocks, the genetic markers, such as Cl, lg, Pn, g, la, bl and gl, showed the segregation of 3 dominance to 1 recessiveness, and the Bh gene segregation fitted well to the 9:7. The rest 4 genetic markers, such as gh, Lh, nl and be, did not show the good fitness to the expected ratio. The resistance genes Wbphl of N22 and the Wbph2 of ARC 10239 appeared to be single dominant gene each. The Wbphl gene was linked with the marker gene, liguleless (lg) of linkage group II with the recombination value of 36.8%, and with the black hull (Bh) with the value of 35.9%. The Wbph2 gene appeared to be independent of all the markers tested here, such as Cl, lg, Pn, g, Lh, la, nl, bl, bc, gl, Bh, of linkage gtoup I, II, III, IV, VI, VII, VIII, IX, X, XI, and XII respectively. That the Wbph2 linkage relations were not investigated was regarded as the causes that the tested marker genes on the chromosome were located with the resistance gene at the distant loci, and of the phenctypic properties of the marker characters. The Wbph2 linkage relations should be reexamined in the cross combinations of linkage group Ⅶ, Ⅷ, Ⅹ and XII including linkage group V which was not tested in this experiment.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.11
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• pp.1519-1523
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• 2006

Through a screening and selection approach method, decamer random markers were used in a technique called random amplified polymorphic DNA (RAPD) assay with 252 genomic DNAs isolated from four major Haimen chicken populations: Rugao (62), Jiangchun (62), Wan-Nan (63) and Cshiqishi (65). A total of 3-score decamer random primers (S241-S260, S1081-S1100 and S1341-S1360) were employed in the preliminary RAPD-polymerase chain reaction (RAPD-PCR) assay with 50 random template DNA samples from all the populations. Four (6.67%) of the primers that produced obvious polymorphic patterns, interpretable and reproducible bands were selected and used with both the individual DNAs from each population and with pooled DNA samples of the four populations in subsequent analyses. The selected primers produced a total of 131 fragments with molecular size ranging from 835 to 4,972 base pairs (bp) when used with the individual DNAs; 105 (80.15%) of these fragments were polymorphic. With the pooled DNAs, 47 stable and characteristic bands with molecular size ranging from 840 to 4,983 bp, of which 23 (48.94%) polymorphic, were also generated. The band-sharing coefficient (BSC) calculated for the individuals in the population and among populations of bulked samples was between 0.8247 (Rugao) and 0.9500 (Cshiqishi); for pairwise populations, it was between 0.7273 (Rugao vs. Wan-Nan) and 0.9367 (Jiangchun vs. Cshiqishi) chicken populations. Using the BSC for individual and pairwise populations, the Nei's standard genetic distances between the chicken populations were determined and ranged from 0.0043 (Jiangchun vs. Cshiqishi) to 0.1375 (Rugao vs. Cshiqishi). The reconstructed dendrogram linked the Jiangchun and Cshiqishi chickens as closely related populations, followed by Wan-Nan, while the Rugao was the most genetically distant among the populations.

• Journal of Life Science
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• v.14 no.3
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• pp.425-428
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• 2004

Molecular authentication and genetic polymorphism of Korean ginseng cultivars and accessions were investigated using ISSR (inter-simple sequence repeat amplification) markers. Five primers among 56 produced clear and reproducible DNA fragments among seven cultivars and accessions. A total of 43 bands ranging from 250 bp to 1,700 bp from five primers were scored. Average number of bands per primer was 8.6 and only nine bands were polymorphic across the six Panax ginseng from Korea. Especially Chunpoong cultivar exhibited the highest level of polymorphism, whereas other accessions did not showed almost any polymorphism. Consequently, these ISSR markers will be available to differentiate Chunpoong cultivar from other major Korean ginseng cultivars and accessions, such as Yunpoong, Hwangsukjong and Jakyungjong, at the DNA level.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.45 no.4
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• pp.227-231
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• 2000

Small seed size is one of the major traits of soybean cultivars for sprouts with regard to high sprout yield. This study was conducted to identify quantitative trait loci (QTL) for seed size and weight in a set of F 6 seeds of 89 lines derived from a cross between 'Pureunkong', a soybean cultivar developed for sprouts and 'Jinpumkong 2', a soybean cultivar with no beany taste in seed due to the lack of lipoxygenases. The genetic map of 25 linkage groups with a total of 98 markers including RFLP, RAPD, SSR and classical markers was constructed from this F/sbu 5/-derived population and was used for QTL analysis. 'Pureunkong' was significantly smaller (P＜0.01) than 'Jinpumkong 2' in seed size and seed weight. Genetic variation was detected and transgressive segregation was common in the population for these traits. Seven DNA markers including opT14-1600 in LG A2, opF02-400 in LG B2, Satt100, opC09-700, opG04-730 and opQll-650 in LG C2, and opY07-1100 ＆ 1000 in LG(unknown) were significantly associated and accounted for 4.7 to 10.9% and 5.1 to 10.1 % of the phenotypic variation in seed size and seed weight, respectively. 'Pureunkong' alleles increased seed size and seed weight at the all four significant marker loci on the LG C2. These marker loci in LG C2 were closely linked and were presumed to be a single QTL. Overall, at least three independent QTLs from 3 linkage groups (A2, B2, and C2) were putatively involved in the control of seed size and seed weight.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.1
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• pp.69-72
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• 2004

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.745-752
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• 2014

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is an economically important vegetable crop as a source of the traditional food Kimchi in Korea. Although many varieties exhibiting desirable traits have been developed by the conventional selective breeding approach, breeding related to abiotic or biotic stresses, such as a particular pests or diseases, or tolerance to climatic conditions, is likely to be slow. This could be helped by an efficient method for selection from various, rapidly-evolved genetic resources on the basis of molecular markers. In particular, the Brassica genome sequencing project enables genome-wide discovery of genes or genetic variants associated with agricultural traits. We here discuss the recent progress in the field of Chinese cabbage breeding with regard to the application of molecular markers.

• Korean Journal of Plant Tissue Culture
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• v.25 no.5
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• pp.309-313
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• 1998

RAPD (Random Amplified Polymorphic DNA) analysis was conducted to Schisandra nigra plants in order to select the specific markers for monoecious and dioecious individuals. RAPD results using eighty random 10-mer primers revealed that S. nigra had a different banding pattern from S. chinensis and Kadsura japonica. When DNA isolated from leaves of monoecious and dioecious plants were used as PCR template, only five primers, OPA-17, OPA-19, OPB-03, OPB-09 and OFB-16, showed polymorphic band patterns. No variation in banding profiles within male or female individuals was observed when these five primers were used whereas three monoecious plants (No 1, No 2 and No 3) showed different banding patterns one another, A 750 bp segment was amplified by primer OPB-3 from male individuals. On the other hand, two segments, 950 bp and 1690 bp, with OPA-19 and 700 bp of segment with OPB-3 were amplified in female individuals. These result indicate that the specific buds of male and female S. nigra could be used as genetic markers for the early discrimination of male and female individuals.

• Molecules and Cells
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• v.26 no.3
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• pp.250-257
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• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.