• Korean Journal of Breeding Science
• /
• v.40 no.2
• /
• pp.119-127
• /
• 2008

A total of 41 microsatellite markers were used with 29 genotypes to examine the relationship between SSR polymorphisms and N-use efficiency related traits with a goal to identify the putative QTLs related to these traits. These primers yielded a total of 183 alleles (average 4.46 alleles per primer), and polymorphism information content (PIC) values of the SSRs ranged from 0.119 to 0.805 with mean value of 0.425. Correlation coefficients were obtained among the four N-use efficiency traits in the 34 accessions and significant positive correlations of relative ratios between grain yield and harvest index (r=0.3404) and total dry matter (r=0.7976), while N uptake showed a moderate level of correlation with the ratios of the grain yield and total dry matter, respectively. 36.5% (15/41) SSR markers were monomorphic among the 25 japonica accessions out of the 29 accessions. Association between SSR genotypes and phenotypic performances from the total (29) or japonica (25) accessions was tested based on a single point analysis. Three putative QTL regions were detected for the ratio of grain yield. These include the chromosomal region containing the RM283 locus on chromosome 1 and RM25 on chromosome 8 (all and japonica accessions) and the region with the SSR marker, RM206 on chromosome 11 (the japonica accessions). For the total dry matter ratio, two chromosomal regions were identified as the putative QTL region. One is the region with the SSR marker, RM162 on chromosome 6 (all and japonica accessions) and the other was the one with the SSR marker RM25 on chromosome 8 (the japonica accessions). Among these markers, RM25 showed associations with both traits.

• Journal of Korean Society of Forest Science
• /
• v.102 no.1
• /
• pp.59-65
• /
• 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 Life Science
• /
• v.14 no.2
• /
• pp.339-344
• /
• 2004

Identification of individual quantitative trait loci (QTL) is a prerequisite to application of marker-assisted selection for stern length. Two simple sequence repeat (SSR)-based linkage maps were constructed from recombination inbred line populations between cross of Keunolkong and Shinpaldalkong. Two parents used differed greatly in stem length, which were 30.57 cm and 49.75 cm in Keunolkong and Shinpaldalkong, respectively. Using the constructed maps, regression analysis and interval mapping were performed to identify QTLs conferring stem length. Four QTLs for stem length on linkage groups (LG) F, J, N and O were identified in the Keunolkong ${\times}$ Shinpaldalkong population and they totally explained 37.83% of variation for stem length. In the population, two major QTLs on LG J and O conditioning 14.25% and 10.68% of the phenotypic variation in stem length were determined and two QTLs with minor effect were detected on LG F and N. Identification of QTLs for stem length and mapping individual locus should facilitate to describe genetic mechanisms for stem length in different population. SSR markers tightly linked to QTLs for stem length allow to accelerate the elimination of deleterious genes and selection for desirable recombinants at early stage in crop breeding programs.

• Journal of Korean Society of Forest Science
• /
• v.102 no.2
• /
• pp.264-271
• /
• 2013

Mating system parameters were estimated in a natural population of Pinus koraiensis which was located at Gwongeumseong in Mt. Seorak, South Korea. The estimated parameters from allozyme were as follows: 0.882 of multilocus outcrossing rates($t_m$), 0.881 of singlelocus outcrossing rates($t_s$), 0.368 of correlated paternity($r_p$), and 2.7 of number of effective pollen contributors. The estimated parameters from cpSSR markers were as follows: 0.831 of average of outcrossing rates and 12.4 of the average number of effective pollen contributors. The average outcrossing rate from two genetic markers was 0.857, which was similar to those estimated in other conifer species. More number of potential pollen contributors was estimated from cpSSR marker analysis compared with that estimated from allozyme marker analysis. This result sugges$t_s$ that cpSSR markers may be more useful than allozyme markers for identifying potential pollen contributors in the analysis of mating system.

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

• Journal of Ginseng Research
• /
• v.36 no.3
• /
• pp.298-307
• /
• 2012

Panax ginseng has been cultivated for centuries, and nine commercial cultivars have been registered in Korea. However, these nine elite cultivars are grown in less than 10% of ginseng fields, and there is no clear authentication system for each cultivar even though their values are higher than those of local landraces. Here, we have developed 19 microsatellite markers using expressed gene sequences and established an authentication system for all nine cultivars. Five cultivars, 'Chunpoong', 'Sunpoong', 'Gumpoong', 'Sunun', and 'Sunone', can each be identified by one cultivar-unique allele, gm47n-a, gm47n-c, gm104-a, gm184-a (or gm129-a), and gm175-c, respectively. 'Yunpoong' can be identified by the co-appearance of gm47n-b and gm129-c. 'Sunhyang' can be distinguished from the other eight cultivars by the co-appearance of gm47n-b, gm129-b, and gm175-a. The two other cultivars, 'Gopoong' and 'Cheongsun', can be identified by their specific combinations of five marker alleles. This marker set was successfully utilized to identify the cultivars among 70 ginseng individuals and to select true F1 hybrid plants between two cultivars. We further analyzed the homogeneity of each cultivar and phylogenetic relationships among cultivars using these markers. This marker system will be useful to the seed industry and for breeding of ginseng.

• Molecules and Cells
• /
• v.24 no.1
• /
• pp.60-68
• /
• 2007

Microsatellites, also called simple sequence repeats (SSR), are very useful molecular genetic markers commonly used in crop breeding, species identification and linkage analysis. In the present study, we constructed a microsatellite-enriched genomic library of Panax ginseng, and identified 251 novel microsatellite sequences. Tri-nt repeat units were the most abundant (46.6%), followed by di-nt repeats (35.5%). The $(AG)_n$ motif was most common (23.1%), followed by the $(AAC)_n$ motif (22.3%). From the genotyping of 94 microsatellites using marker-specific primer sets, we identified 11 intraspecific polymorphic markers as well as 14 possible interspecific polymorphic markers differing between P. ginseng and P. quinquefolius. The exact allele structures of the polymorphic markers were determined and the alleles were named. This study represents the first report of the bulk isolation of microsatellites by screening a microsatellite-enriched genomic library in P. ginseng. The microsatellite markers could be useful for linkage analysis, genetic breeding and authentication of Panax species.

• The Plant Pathology Journal
• /
• v.32 no.2
• /
• pp.95-101
• /
• 2016

Inheritance of resistance to Fusarium wilt (FW) disease caused by Fusarium udum was investigated in pigeonpea using four different long duration FW resistant genotypes viz., BDN-2004-1, BDN-2001-9, BWR-133 and IPA-234. Based on the $F_2$ segregation pattern, FW resistance has been reported to be governed by one dominant gene in BDN-2004-1 and BDN-2001-9, two duplicate dominant genes in BWR-133 and two dominant complimentary genes in resistance source IPA-234. Further, the efficacy of six simple sequence repeat (SSR) markers namely, ASSR-1, ASSR-23, ASSR-148, ASSR-229, ASSR-363 and ASSR-366 reported to be associated with FW resistance were also tested and concluded that markers ASSR-1, ASSR-23, ASSR-148 will be used for screening of parental genotypes in pigeonpea FW resistance breeding programs. The information on genetics of FW resistance generated from this study would be used, to introgress FW resistance into susceptible but highly adopted cultivars through marker-assisted backcross breeding and in conventional breeding programs.

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

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