• Journal of Life Science
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• v.16 no.6
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• pp.1001-1005
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• 2006

The objective of this study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for genetic diversity assessment and identification of rice varieties. The 23 primers selected from 50 SSR primers showed polymorphisms in the 21 rice varieties. The 2 to 9 SSR alleles were detected for each locus with an average of 3.00 alleles per locus. The polymorphism information content (PIC) ranged form 0.091 to 0.839. Based on band patterns, UPGMA cluster analysis was conducted. These varieties were separate into 4 groups corresponding to rice ecotype and pedigree information and genetic distance of cluster ranging from 0.59 to 0.92. The 4 SSR primer sets (RM206, RM225, RM418, RM478) selected form 23 polymorphic primers were differentiated all the rice variety from each other by markers genotypes. These markers may be used wide range of practical application in variety identification of rice.

• Korean Journal of Plant Resources
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• v.26 no.4
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• pp.491-502
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• 2013

Persimmon (Diospyros kaki Thunb) fruit is one of the most important fruit and have been cultivated from ancient times in Korea. In this study, we found 16 EST-SSR markers that contained one or more EST-SSR sites from 246 cDNA sequences. The developing of EST-SSR marker analysis from 42 persimmon cultivars was compared by genetic relationships and morphological relationships using 6 qualitative traits (fruit related 6 traits) and 19 quantitative traits (flower related 19 traits). In this study, 25 primer sets were tested to identify PCR polymorphism and 14 potential EST-SSR primer pairs were selected. The result of morphological relationship EST-SSR marker analysis showed that the coefficient 0.02 was difficult to categorize in several groups. And then, coefficient 0.77 of genetic relationship showed that the group was classified as four groups. The result of correlation distance between genetic relationship and morphological relationship were investigated was low significance (-0.03). Our results also provided an optimized method for improvement of breeding efficiency and introduce of superior character at persimmon cultivars using EST-SSR markers which was useful for further investigation.

• Journal of Korean Society of Forest Science
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• v.99 no.3
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• pp.344-352
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• 2010

To investigate the mating system of clones in the seed orchard of Japanese red pine, parameters of mating system, such as outcrossing rates, number of potential pollen contributors, and degree of pollen contamination, were estimated in the seed orchard of Japanese red pines on the basis of DNA data including 4 nSSR and 6 cpSSR markers. Estimates of outcrossing rates were ranged from 94.9 to 100% with an average of 98.9% on the basis of the analysis of cpSSR haplotypes. They were ranged from 90.3% to 100% with an average of 95.9% on the basis of the analysis of nSSR genotypes. However, cross checking of both DNA markers revealed that the seeds presumed to be products of self pollination were turned out to be generated by pollination between mother tree and other tree (i.e., 100% of cumulative outcrossing rate). Estimates of pollen contamination ranged from 43.6% (Gangwon-10) to 56.4% (Gangwon-12) with the average of 48.9%. On the basis of pooled cpSSR haplotype of each seed, maximum number of 21 pollen contributors were verified from the seeds reproduced by Kyungbuk-38. Minimum number of 13 pollen contributors were verified in Gangwon-10. Mean of 16.2 pollen contributors were verified from a total of 5 mother trees. In conclusion, considering pretty high outcrossing rates between clones within a seed orchard, it may be expected that a fairly good genetic potential of the seeds, produced in '77 plot of the seed orchard of Japanese red pines at Anmyeon island, may be guaranteed. Observed results from the analysis of mating system of Japanese red pines in a '77 plot of the seed orchard may also provide useful information for the establishment and management of the seed orchard of the progressive generation.

• 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.18 no.4
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• pp.323-330
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• 2020

Agaricus bisporus is an important edible mushroom that is used as a functional food. In this study, European A. bisporus strains were analyzed for genetic diversity, population structure, and genetic differentiation using simple sequence repeat (SSR) markers. European A. bisporus strains were divided into four groups by distance-based analysis and two subpopulations by model-based analysis. The SSR markers used in this study did not group European A. bisporus strains by geographical region or pileus color. Genetic diversity was high in Group 4 based on distance-based analysis and Pop. 2 based on model-based analysis. A. bisporus strains showed very low genetic differentiation. The results of this study can be used for breeding A. bisporus in the future.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.48 no.1
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• pp.56-64
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• 2003

If a quantitative trait loci (QTL) marker identified in a population is applicable to different populations (marker universality), this will not only reduce the labor and cost in marker assisted selection (MAS), but accelerate the application of molecular markers to real breeding programs. Present study aims to evaluate the defined QTL related markers from a population to a different breeding population for the MAS. Four rice breeding populations were subjected to seventy-five simple sequence repeat (SSR) markers which were already identified for their polymorphism information content (PIC) in the parents of the crossings. Among them, eight markers were evaluated for their correlation between presence of marker alleles and phenotypic expression in breeding populations. A reasonable level of polymorphism for the mapped markers originated from any sources of rice accessions was observed between crosses of any sources (marker repeatability). However, correlation between presence of markers and expression of the traits in rice breeding populations was not significant except for minor portion of traits and markers examined (failure of marker universality). In the present study, various strategies were discussed to develop new markers with universality of breeding application.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.337-343
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• 2013

The aims of this study were to compare genetic distances among 14 Phalaenopsis varieties using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) marker systems and to determine the discrimination using SSR. A total of 111 SSR primers and 30 SRAP combinations were initially screened. Twelve SSR primers and thirty SRAP combinations showed high polymorphism among the 14 Phalaenopsis varieties including domestic breeding varieties, conserved in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected by silver staining method. A total of 474 polymorphic bands, including 55 by SSRs and 419 by SRAPs, were identified and used for genetic diversity analysis. Polymorphic bands were scored for calculating a simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. Fourteen Phalaenopsis varieties were classified into three major groups at similarity coefficient value of 0.683 and 0.66 using SRAP and SSR, respectively. Also we could discriminate these domestic breeding Palaenopsis varieties using only SSR 20 and SSR 22. The results indicate that SSR analysis is effective for discrimination among Phalaenopsis varieties and SRAP is useful for genetic diversity when there is no sequence information. These studied SSR and SRAP markers will be useful tools for genotype identification, germplasm conservation and genetic relationship study in Phalaenopsis.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.2
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• pp.231-240
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• 2009

A total of 26 Korean elite soybean cultivars including 21 certified cultivars was assessed to evaluate genetic diversity and to analyze relationship among them based on 15 SSR markers. Fifteen SSR markers generated a total of 201 alleles. Average number of alleles per SSR marker was 13.4 with a range from 8 to 19. Genetic diversity of 26 cultivars estimated by PIC value ranged from 0.782 to 0.931 with an average of 0.874. PIC value of Satt197 was the highest with 0.931 and Satt141 was the lowest with 0.782 among 15 SSR markers. Cluster analysis based on genetic distances classified 26 soybean cultivars into 3 clusters. Cluster I, II and III included 2, 7 and 17 cultivars, respectively. Average genetic diversity within clusters was 0.769 with a range from 0.720 to 0.799. Average genetic diversity between clusters was 0.813 with a range from 0.725 to 0.857. Genetic diversity was higher between clusters than within clusters. Genetic relationship among clusters was near between I and II, and I and III and far between II and III cluster. All of 26 Korean elite soybean cultivars could be identified by using any of 5 combinations of 2 SSR markers with higher PIC value, i.e, $Satt197+Sat_088$, Satt197+Satt245, $Sat_088+Sat_-036$, $Sat_088+Satt245$ and Satt185+Satt245.

• Journal of Plant Biotechnology
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• v.31 no.3
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• pp.179-184
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• 2004

A doubled-haploid (DH) population was developed through anther culture of F$_1$ plants obtained from a cross between a japonica cultivar, 'Nagdongbyeo', as male parent and a indica cultivar, 'Samgangbyeo', as female parent. Segregation modes for plant length, culm length, panicle length, third internode length, and days to heading in the DH lines showed nearly normal distribution with wide range of variation. A molecular map with 136 simple sequence repeat (SSR) markers was constructed using the DH population. The total map distance was 1,909 cM and the average interval of marker distance was 14 cM.

• Journal of Ecology and Environment
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• v.37 no.1
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• pp.21-29
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• 2014

Robinia pseudoacacia has become invasively naturalized in Japan. We investigated the role of sexual reproduction in the development of R. pseudoacacia riparian forests along the Chikumagawa River in Japan, by using five chloroplast (cpSSR) and seven nuclear (nSSR) markers. We identified eight chloroplast haplotypes and 147 nuclear genotypes from 619 R. pseudoacacia trees sampled in three plots (Plots A, B, and C) and along two line transects (Lines D and E). CpSSR analyses showed that multiple maternal lines were distributed along the river, and that some haplotypes from different populations overlapped. In addition, while Plots A and B were separated by a short distance, only these two plots exhibited genetic differentiation in the haplotypes. In the nSSR analysis, all pairwise $F_{ST}$ values among the three plots were significantly different from zero. Kinship analysis based on nSSR markers revealed that kinship connected many individuals to another individual from the same plot. These results indicate that seed dispersal near to mother trees contributes to the fine-scale genetic structure of R. pseudoacacia riparian forests. Our results indicate that sexual reproduction, in addition to asexual reproduction, is a major contributor to the fine-scale formation of R. pseudoacacia forests.