• Journal of Korean Society of Forest Science
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• v.102 no.1
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• pp.59-65
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• 2013

The jujube is an important fruit tree species in Korea. Traditionally, classifications of jujube cultivars have been based on morphological characters; however, morphological identification can be problematic because morphological traits are affected by environmental conditions. Therefore, DNA markers are now being used for the rapid and accurate identification of plant species. Inter-simple sequence repeat (I-SSR) is one of the best DNA-based molecular marker techniques, which is useful for studying genetic relations and for the identification of closely related cultivars. In this study, 5 Korean jujube trees and 1 jujube tree imported from China were analyzed for 16 I-SSR primers. Amplification of the genomic DNA of jujube cultivars by using I-SSR analysis generated 100 bands, with an average of 6.25 bands per primer, of which 45 bands (45%) were polymorphic. The number of amplified fragments with I-SSR primers ranged from 2 to 13. The percentage of polymorphism ranged from 10% to 100%. I-SSR finger printing profiles showed that 'Boeun jujube' and 'Daeri jujube' had characteristic DNA patterns, indicating unequivocal cultivar identification at molecular level. According to the results of clustering analysis, the genetic similarity coefficient ranged from 0.68 to 0.92. 'Boeun jujube' and 'Daeri jujube' were divided into independent groups, and 'Bokjo jujube', 'Geumseong jujube', 'Wolchul jujube', and 'Mudeung jujube' were placed in the same group. Therefore, I-SSR markers are suitable for the discrimination of 'Boeun jujube' and 'Daeri jujube' cultivars.

• Journal of Korean Society of Forest Science
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• v.89 no.4
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• pp.536-542
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• 2000

A linkage map for Japanese red pine (Pinus densiflora) was constructed on the basis of two DNA marker systems of random amplified polymorphic DNAs (RAPDs) and inter-simple sequence repeats (I-SSR). Haploid genomic DNAs were extracted from megagametophyte tissues of 96 individual seeds in a single tree. A total of 98 DNA markers including 52 RAPD markers amplified by 25 primers and 46 I-SSR markers amplified by 18 primers were verified as Mendelian loci showing 1 : 1 segregation in 96 megagametophytes which were ${\chi}^2$-tested at 5% significance level. Of them, 63 segregating loci turned out to be linked into 20 linkage groups by the two-point analysis. However, 35 loci (17 RAPD and 18 I-SSR) of the 98 segregating loci did not coalesced into any linkage groups at a LOD of 3.0. The linked 63 loci were separated by an average distance of about 25.5 cM, which were spanned 1097.8 cM as a whole. The minimum and maximum map distances of the linkage groups were 4.3 cM and 54.9 cM, respectively. Incorporation of I-SSR loi into linkage map of RAPD loci resulted in extended and partially more saturated linkage blocks.

• Journal of Korean Society of Forest Science
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• v.95 no.4
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• pp.435-442
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• 2006

A total of 167 peculiar haplotypes confirmed from 28 cpSR variants that were observed in 19 populations of Japanese red pine in Korea through cpSSR marker analysis. Thirteen individuals that showed identical haplotype dispersed evenly in 10 populations, and the average number of effective haplotype within population was 13.37. Estimate of genetic diversity (He) was 0.987 on the basis of cpSSR haplotype variants that was equivalent to or higher than the estimates reported in other studies on some forest tree species. Estimation of genetic diversity (S.I.) on the basis of cpSSR variants composing each haplotype revealed the highest estimate of 1.109 for the population of Gangwon-Yeongwol and the lowest estimate of 0.411 for the population of Gyeongbuk Mungyeong with the average of 0.887. Most of observed cpSSR variants appeared to exist commonly in 19 populations (97.62%), and genetic differentiation of cpSSR variants among populations was turned out to be weak (${\Phi}_{ST}=0.024$). Relatively fast rate of mutation of cpSSR marker might be a major cause for such weak population differentiation. There was no identical haplotype shared between 39 population pairs of 173 pair-wise population pairs. Estimation of genetic distance among 19 populations on the basis of population pairs was also impossible, that might be resulted from restricted migration among 19 populations. Considering the observed distribution patterns of cpSSR variants in addition to the previous studies on I-SSR variants, informations on the present geographic location and genetic status of populations should be considered together for effective sustainable management of the genetic resources of Japanese red pine in Korea.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.142-153
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• 2016

The present study investigated identification of cultivars through phylogenetic analysis of 108 Citrus varieties and related cultivars using simple sequence repeat (SSR) markers. Two hundred three SSR primer pairs were used to detect polymorphic markers among 8 Citrus cultivars consisting of 4 mandarins, 1 orange, 1 tangor, 1 tangelo, and 1 pumelo. Eighteen SSR primer pairs were reproducible and showed highly polymorphic alleles. These markers were applied to assess genetic variations of the 108 varieties. Each marker detected 5-14 alleles, with an average of 9.28. The polymorphism information content varied from 0.417 to 0.791 with an average of 0.706. Cluster analysis with SSR markers resulted in 13 major groups reflecting cultivar types and pedigree information. Twelve orange cultivars in the $I-1^{st}$ sub-cluster and 23 mandarin cultivars in the $II-1^{st}$ sub-cluster, respectively, were not discriminated using the SSR markers. This could be due to narrow genetic backgrounds originated through bud mutation or nucellars seedlings. The SSR profile database of Citrus cultivars will be useful as a tool for protection of plant breeders' intellectual property rights in addition to assessing genetic diversity in Citrus cultivars and germplasms.

• Horticultural Science & Technology
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• v.32 no.1
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• pp.84-90
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• 2014

Berchemia racemosa var. magna is only found in Anmyeon Island of South Korea. Genetic diversity and the spatial genetic structure of B. racemosa var. magna in Anmyeon Island were studied by I-SSR marker system. Fifty I-SSR amplicons were produced from 8 selected primers. We used 13 polymorphic markers to analyze the genetic structure. Distribution of 39 individuals in the study plot($90m{\times}70m$) showed aggregate pattern (aggregation index = 0.706). Total 21 genets were observed from 39 individuals through I-SSR genotyping. Proportion of distinguishable genotype (G/N), genotype diversity (D) and genotype evenness (E) were 53.8%, 0.966 and 0.946, respectively. In spite of the small number and the narrow distribution, Shannon's diversity index (I = 0.598) was relatively high as compared with those of the other plant species. For ex situ genetic conservation of B. racemosa var. magna, the sampling strategy based on spatial autocorrelation using Tanimoto distance is efficient at choosing the conserved individuals with a 6 meter interval between individual trees.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.273-281
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• 2011

Fusarium head blight (FHB), also known as scab, caused mainly by Fusarium graminearum is a devastating disease of wheat in regions that are warm and humid during flowering. In addition to significant yield and quality losses, the mycotoxin deoxynivalenol produced by the pathogen in infected wheat kernels is a serious problem for food and feed safety. Twenty- three Korean cultivars and "Sumai 3", which is a FHB-resistant Chinese cultivar were tested for Type I, Type II resistances of FHB. Three cultivars were identified as resistant in Type I assessment, and two cultivars were resistant in Type II assessment. Genetic variation and relationship among the cultivars were evaluated on the basis of 11 Simple Sequence Repeat (SSR) and 29 Sequence Tagged Site (STS) markers that were linked to FHB resistance Quantitative Trait Loci (QTL) on chromosome 3BS. One SSR and 7 STS markers detected polymorphisms. Especially, using a STS marker (XSTS3B-57), 32.4% of the variation for Type II FHB resistance could be explained. Genetic relationship among Korean wheat cultivars was generally consistent with their released year. These markers on chromosome 3BS have the potential for accelerating the development of Korean wheat cultivars with improved Fusarium head blight resistance through the use of marker-assisted selection.

• Horticultural Science & Technology
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• v.29 no.4
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• pp.366-373
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• 2011

To analyze the genetic relationships among Korean potato cultivars and to develop cultivar identification method using DNA markers, we carried out genotyping using simple sequence repeats (SSR) analysis and developed multiplex-SSR set. Initially, we designed 92 SSR primer combinations reported previously and applied them to twenty four Korean potato cultivars. Among the 92 SSR markers, we selected 14 SSR markers based on polymorphism information contents (PIC) values. PIC values of the selected 14 markers ranged from 0.48 to 0.89 with an average of 0.76. PIC value of PSSR-29 was the lowest with 0.48 and PSSR-191 was the highest with 0.89. UPGMA clustering analysis based on genetic distances using 14 SSR markers classified 21 potato cultivars into 2 clusters. Cluster I and II included 16 and 5 cultivars, respectively. And 3 cultivars were not classified into major cluster group I and II. These 14 SSR markers generated a total of 121 alleles and the average number of alleles per SSR marker was 10.8 with a range from 3 to 34. Among the selected markers, we combined three SSR markers, PSSR-17, PSSR-24 and PSSR-24, as a multiplex-SSR set. This multiplex-SSR set used in the study can distinguish all the cultivars with one time PCR and PAGE (Polyacrylamide gel electrophoresis) analysis and PIC value of multiplex-SSR set was 0.95.

• Plant Resources
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• v.6 no.1
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• pp.16-26
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• 2003

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Present study was conducted to evaluate the genetic diversity within a diverse collection of rice accessions used for Korean breeding programs. Two hundred eighty-seven rice cultivars, composed of temperate japonica, tropical japonica, indica, and Tongil-type of Korean crossing parents were evaluated by means of 15 simple sequence repeat (SSR) markers. A total of 99 alleles were detected, and the number of alleles per marker ranged from 4 to 11, with an average of 6.6 per locus. Polymorphism information content (PIC) for each of the SSR markers ranged from 0.2924 to 0.8102 with an average of 0.5785. These results, with the result that use of only 15 SSR markers made all rice cultivars examined could be uniquely distinguished, imply the efficiency of SSR markers for analysis of genetic diversity in rice. Cluster analysis was performed on similar coefficient matrics calculated from SSR markers to generate a dendogram in which two major groups corresponding to japonica (Group I) and indica and Tongil type rice (group II) with additional subclasses within both major groups. The narrowness of the Korean breeding germplasm was revealed by the fact that most of the Korean-bred and Japan-bred temperate japonica cultivars were concentrated into only 2 of the sub-group I-1 (143 cultivars) and I-2 (58 cultivars) among six sub-groups in major group of japonica. This is because of the japonica accessions used in this study was a very closely related ones because of frequent sharing of the crossing parents with similar genetic background with synergy effect of the inherited genetic difference between indica and japonica. A rice breeding strategy with the use of molecular markers was discussed for overcoming of genetic vulnerability owing to this genetic narrowness.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.87-99
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• 2010

Genetic diversity and relationships within and among Korean, Japanese and Chinese Jilin provincial wild soybeans based on SSR markers were evaluated to enlarge genetic variation in soybean breeding in the future. A total of 184 wild soybeans including 67 Korean, 71 Japanese and 46 Chinese Jilin provincial wild soybeans were analyzed to evaluate genetic diversity and relationships based on 23 SSR markers. Korean and Japanese wild soybeans were obtained from National Agrobiodiversity Center, Korea, and Biological Resource Center in Lotus and Glycine, Frontier Science Research Center, University of Miyazaki, Japan, respectively. Chinese wild soybeans were collected from Jilin province, China. Twenty three SSR markers generated a total of 964 alleles with an average of 41.9 alleles per marker. Number of alleles ranged from 23 (Satt635) to 56 (Satt157). Genetic diversity (PIC value) of 184 wild soybeans ranged from 0.880 to 0.968 with an average of 0.945. Number of alleles for Korean, Japanese and Chinese Jilin provincial wild soybeans was 513 with an average of 22.3, 511 with an average of 22.2, and 312 with an average of 13.6 per marker, respectively. PIC value for Korean, Japanese and Chinese Jilin provincial wild soybeans was similar with an average of 0.905, 0.897, and 0.850, respectively. Cluster analysis based on genetic distances estimated by SSR markers classified wild soybeans into 3 clusters. Cluster I included only Chinese Jilin provincial wild soybeans. Cluster II included most of Japanese wild soybeans including 5 Korean wild soybeans. Cluster III included most of Korean wild soybeans including 6 Japanese and 1 Chinese Jilin provincial wild soybeans. Cluster I was not subclassified, but cluster II and III were subclassified into various groups. Genetic distance evaluated by SSR markers between Korean and Japanese wild soybeans was closer than that of between Korean and Chinese Jilin provincial, and between Japanese and Chinese Jilin provincial wild soybeans.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.405-412
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• 2011

Knowledge of genetic diversity and genetic relationships among inbred lines gives a significant impact on the selection of parental lines for hybrid maize varieties. Genetic diversity and genetic relationships among 86 popcorn inbred lines were analyzed using 50 SSR markers distributed over the whole genome. A total of 256 alleles were identified at all the SSR loci with an average of 5.1 and a range between two and sixteen per locus. The gene diversity values varied from 0.21 to 0.831 with an average of 0.579. The cluster tree generated using the described SSR markers recognized three major groups at 35.8% genetic similarity. Groups I, II, III respectively included 40, 39 and 7 inbred lines. The present study indicates that the SSR markers chosen for this analysis are effective for the assessment of genetic diversity and genetic relationships among 86 popcorn inbred lines in Korea.