• Molecules and Cells
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• v.19 no.3
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• pp.428-435
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• 2005

This study was carried out to assess the potential of SSR markers for variety identification by comparing SSR markers and morphological traits in tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Twenty-seven SSR markers were polymorphic in 66 pepper varieties, revealing a total of 89 alleles. Average polymorphism information content (PIC) value was 0.529, ranging from 0.03 to 0.877. Cluster analysis of the band patterns separated the varieties into three groups corresponding to varietal types. Morphological trait-based clustering showed some degree of similarity to dendrogram topologies based on the SSR index. However, no significance correlation was found between the SSR and morphological data. SSR markers could be used to complement a DUS test of a candidate variety and to select complimentary varieties by pre-screening existing varieties in the context of protecting new varieties of pepper.

• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.217-227
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• 2018

Gummy stem blight (GSB) is one of the most destructive and economically important, soil borne diseases of melon caused by the ascomycete fungus, Didymella bryoniae throughout the world. In Korea, however, no GSB resistant genotype has been reported yet. The study aimed to identify GSB resistant melon germplasm. We screened a total of 60 genotypes including 16 lines and 44 melon cultivars collected from USA and Korea. Among the 16 melon lines, four lines including 'PI482399', 'PI140471', 'PI136170' and 'PI420145', and two Korean cultivars viz. 'Asia Papaya' and 'Supra' showed complete resistance. We were aware that both genotypic and environmental variations could influence the phenotypic screening of resistance and susceptibility. We therefore, further assessed all genotypes using 20 SSR markers. The SSR marker 'CMCT505' linked to Gsb1 in chromosome 1 perfectly grouped resistant and susceptible lines indicating that resistance is probably due to the presence of Gsb1 gene. Cloning and sequencing of resistant and susceptible Gsb1 amplicons showed that there were 32-bp deletions in resistant line and 39-bp deletions in resistant cultivar compared to susceptible one. Thus, the resistant melon lines and cultivars identified in this study could be recommended for the melon breeding program. Furthermore, the SSR marker 'CMCT505' which is tightly linked with Gsb1 could be used for molecular screening of melon germplasm.

• 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.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.181-188
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• 2016

In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata. We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

• Journal of Mushroom
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• v.19 no.1
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• pp.76-80
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• 2021

To develop a method for the differentiation of Pleurotus ostratus cultivars, the multiplex-simple sequence repeat (SSR) primer set based on the SSRs obtained from whole genomic DNA sequence analysis was designed with two polymerase chain reaction (PCR) primer sets. These SSR primer sets were employed to distinguish 10 cultivars and strains. Twenty polymorphic markers were selected based on the genotyping results. PCR with each primer produced 1-4 distinct bands ranging in size from 150 to 350 bp, which was within the expected range. However, since a sole SSR marker was unable to detect polymorphisms in every cultivar, multiplex PCRs with composite PCR primer sets were employed. The multiplex primer, "166+115," completely discriminated 12 cultivars and strains with 40 loci, which were 12 more than the simple arithmetic addition of each locus of the primers 115 and 166. These results might be useful to provide an efficient method for the differentiation of P. ostreatus cultivars with separate PCRs for the quality control of spawn and protection of breeders' rights.

• Korean Journal of Plant Resources
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• v.25 no.1
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• pp.63-71
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• 2012

To assess parameters of mating system in seed orchard, such as outcrossing rates, number of potential pollen contributors, and degree of pollen contamination, seeds, produced in '77 plot of the Japanese red pine (Pinus densiflora S et Z) seed orchard at Anmyeon island, were collected in 2007 and analysed by nSSR and cpSSR markers. Estimates of outcrossing rates ranged from 91.2 to 100% (mean 97.7%) on the basis of the analysis of cpSSR haplotypes and from 81.6 to 100% (mean 95.3%) on the basis of the analysis of nSSR genotypes. By cross checking of both DNA markers, seeds, presumed to be products of self pollination on the basis of single marker, were confirmed as outcrossed seeds, which resulted in cumulative outcrossing rates of 98.9%. On the basis of pooled cpSSR haplotype of each seed, the number of pollen contributors and paternal contribution rates were estimated as 14.8 and 0.512, respectively. In conclusion, considering pretty high level of outcrossing rates observed in a seed orchard, good genetic potential of the seeds, produced in '77 plot of the seed orchard of Japanese red pines at Anmyeon island, may be guaranteed. Investigated results from the analysis of mating system of Japanese red pines in a '77 plot of the seed orchard may also be expected to provide useful information for the management and establishment of the seed orchard of the progressive generation.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.43-43
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• 2019

The collection, evaluation and conservation of crop germplasm have been treated as one of the basics to breeding program. An understanding of genetic relationships among germplasm resources is vital for future breeding process like yield, quality, and resistance. In the present study, EST-SSR markers were employed to assess the polymorphism and genetic diversity of 192 accessions of Proso millet preserved in the National Agrobiodiversity Center of RDA. We evaluated the efficiency of EST-SSR markers developed for proso millet species. A total of 98 alleles were detected with an average allele number of 4.5 per locus among 192 proso millet millet accessions using 22 EST-SSR markers. The averaged values of gene diversity ($H_E$) and polymorphism information content (PIC) for each EST-SSR marker were 0.362 and 0.404 within populations, respectively. Our results showed the moderate level of the molecular diversity among the proso millet accessions from diverse countries. A phylogenetic tree revealed three major groups of accessions that did not correspond with geographical distribution patterns with a few exceptions. The less correlation between the clusters and their geographic location might be considered due to their type difference. Our study provided a better understanding of genetic relationships among various germplasm collections, and it could contribute to more efficient utilization of valuable genetic resources. The EST-SSR markers developed here will serve as a valuable resource for genetic studies, like linkage mapping, diversity analysis, quantitative trait locus/association mapping, and molecular breeding.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.7
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• pp.658-668
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• 2006

The objective of this study was to develop a technique for the cultivar discrimination using SSR markers in soybean. A total of 91 soybean cultivars developed from 1913 to 2002 in Korea were evaluated by five polymorphic SSR markers (Sat_043, Sat_036, Sat_022, Sat_088 and Satt045). Five SSR markers generated a total of 64 alleles and the number of alleles for each SSR marker ranged from 10 to 15 with average of 12.8. Polymorphic information contents (PIC) by five markers of 91 cultivars were ranged from 0.790 to 0.905 with average of 0.857. A total of 82 cultivars (90%) among 91 soybean cultivars could be individually discriminated by combination of five SSR markers through five step analysis. A cultivar, Buseok, by Sat_043 at the first step, 34 cultivars including Hojangkong by Sat_036 at the second step, 29 cultivars including Dankyeongkong by Sat_022 at the third step, 12 cultivars including Sinpaldalkong 2 by Sat_088 at the fourth step, and 6 cultivars including Saebyeolkong by Satt045 at the fifth step were discriminated. Soybean cultivars which were not discriminated by SSR markers could be discriminated by morphological characteristics.

• Korean Journal of Agricultural Science
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• v.39 no.1
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• pp.9-15
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• 2012

The study was conducted to evaluate the genetic similarity among commercial japonica rice varieties in Korea and China and to develop markers to differentiate between japonica cultivars developed in Korea and China. The genetic similarity and cluster of 38 accessions were analyzed using 47 SSR(simple sequence repeat) markers. The number of alleles by 47 SSR markers ranged from 2 to 9 with an average of 3.6. A total of 169 alleles were detected among these tested rice varieties. The PIC value varied from 0.05 to 0.79 with an average of 0.44. The Chinese japonica cultivars could be differentiated from the japonica cultivars in Korea by combining 2 SSR markers, RM223 and RM266. Cluster analysis showed that 38 tested varieties could be distinguished into japonica and indica based on the genetic distance.

• Plant Resources
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• v.1 no.1
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• pp.26-32
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• 1998

This paper describes the variations in eight agronomic traits in three unadapted local landraces and an inbred cultivar of corn. To compare the agronomic traits in field evaluation with molecular marker evaluation the genotypes of the plant introduction were also checked by 4 microsatellite-SSR loci. The variations of the eight agronomic traits were higher in the local landrades than in the inbred line. which was substantiated by the high genetic variation in the landrades with microsatellite-SSR loci. The level of genetic variation was also different between landraces. Since the genetic evaluation can be easily quantified by the analysis of microsatellite-SSR loci. the threshold level of genetic homogeneity in the population for parental lines in breeding program can be determined and the effort of maintaining the landrace population would be alleviated. As an example in our analysis. the entry from Whachon should not need the same number of selfing generations as the other two landraces to get the level of inbred state. Since this line showed lowest intra-genetic variation within the population.