Eleven RAPD primers were assessed to analyze genetic diversity of Korean wheat varieties and to develop DNA marker for cultivar identification. The average of the number of polymorphic bands was 5.2 and PIC values showed 0.48, respectively. Ten major clades were presented by phylogenetic analysis. Three cultivars containing Uri, Hanbeak and Jonong were distinct from the others in the phylogenetic dendrogram. Seven cultivar-specific fragments were detected from 11 RAPD fingerprinting among 35 wheat cultivars and they were sequenced. Four Korean wheat cultivars, Eunpa, Jopoom, Yeonbaek and Jeokjoong, were identified newly by four markers, 84, 173, 174 and KWSM011. We convince that these new DNA markers are useful for cultivar fingerprinting and are applied to marker-assisted selection in wheat breeding program.

Background : Panax ginseng C.A. Meyer is a perennial herb belongs to the family Araliaceae. Wild-cultivated ginseng (WCG) is a specific type of ginseng in Korea which cultivated on artificial forest cultivation method. To obtain a WCG which is similar to wild ginseng (WG), this method usually performed in a mountain using seeds or seedlings of cultivated ginseng (CG) and WG. WCG is very expensive because it is difficult to cultivate. However, systematic cultivation method have not yet been developed compared to high added value. Furthermore, very high price of WCG caused the problem that Panax notoginseng or Panax quinquefolium are sold as WCG in Korean market. In this study, we analyzed the genetic diversity of WCG collected from five areas in Korea using SSR markers. Methods and Results : WCG samples were collected from five areas in Korea (Bucheon, Cheongju, Hoengseong, Judeok and Ulsan). DNA extraction was performed using CTAB method. SSR markers were collected from the published papers. After test PCR using the markers, one of the primer pair was labeled with fluorescence dye (FAM, NED, PET, or VIC) and GeneScan analysis were performed. DNA amplification was conducted using T-100 Thermal Cycler (Bio-Rad). PCR products were separated by capillary electrophoresis on the ABI 3730 DNA analyzer (Applied Biosystems). Conclusion : Eight SSR markers were collected from the published literature and used for the analysis. From the 8 tested SSR markers, 7 SSR markers showed polymorphism between varieties. GenScan analysis were performed using the selected SSR markers to analyze the phylogenetic relationship of WCG. From the results, WCG cultivated in Korea showed that they have a very diverse genetic background.

Background : Codonopsis lanceolata is a perennial plant of Campanulaceae and mainly distributed in East Asia such as Korea, China, and Japan. C. lanceolata has a unique taste and aroma, and it is rich in minerals such as phosphorus and calcium, and vitamin B1 and B2, so our ancestors used the plant as medicinal herb and edible vegetable. However, systematic cultivation and development of varieties have not been achieved compared to demand or high added value. The genetic diversity and relationship analysis of the plants help to increase the efficiency of breeding through genetic variation. Methods and Results : Ten species of Codonopsis plants were used as materials and DNA was extracted from each 4 individuals per species and quantified at a concentration of 10 ng /㎕. The extracted DNA was pooled by species and PCR was performed using the EST-SSR marker developed based on C. lanceolata in the previous study. PCR amplification was carried out using a denaturation at 94℃ for 30 sec, annealing at 58℃ for 30 sec and extension at 72℃ for 30 sec, repeated for 35 total cycles. The PCR products were separated in a 4% agarose gell at 100 V for 40 min. Conclusion : In this study, C. lanceolata collections was determined among several Codonopsis species using these molecular marker. It is expected that the data of this study can be used as reference for genetic polymorphism analysis and related gene studies of Codonopsis species.

Background : Cucuma longa L., in the family Zingiberaceae, is distributed in tropical and/or sub-tropical regions mainly in India and China. This species is commonly called tumeric, powder is used as medicinal herbs and/or flavor enhancer. It has been cultivated in southern region mainly Jindo. However, it might be possible to extend cultivation region due to rise in average temperature. In order to select superior lines, agronomic characteristics is commonly used. Because this is not the ultimate solution, the DNA marker approach has benefited the modern plant breeding. Therefore an easy approach by using one kind of primer have been developed from random amplification of polymorphic DNA sequences (RAPD) to discriminate effectively between different cultivars of Cucuma species Methods and Results : DNAs were extracted from the harvested roots of Cucuma sp. using DNeasy plant Mini kit (Qiagen, Hilen, Germany). These plants cultivated from GARES (Hamyang) and used for PCR amplification. The relative concentration of the extracted DNA was estimated Nano Drop ND-1000 (NanoDrop Technologies, Wklmington, De, USA) and final DNA concentration was adjusted to 5.5 ng/㎕. In this study 9 primer pairs were tested on 8 Cucuma sp. These primers showed polymorphism in Cucuma sp. The cluster dendogram showed that the similarity coefficients ranged from 0.68 to 0.87, CUR02 turned out to be CUR11, and CUR16 is similar to CUR17. Conclusion : These finding could be used for further research on cultivar development by using molecular breeding techniques and for conservation of the genetic diversity of Cucuma species. These data on polymorphism difference based on RAPD will be give us invaluable breeding information by selection of superior lines.

The morphological characteristics and genetic relationships among 32 germplasms of Zanthoxylum schinifolium and Zanthoxylum piperitum collected from two farms in Korea were investigated. The traits with the most variability were seed color, leaf size, and spine size. The intraspecific polymorphism of Z. schinifolium and Z. piperitum was 96.5% and 60.3%, respectively. The genetic diversity and Shannon’s information index values ranged from 0.11 to 0.33 and 0.19 to 0.50, with average values of 0.26 and 0.42, respectively. Two ISSR primers (UBC861 and UBC862) were able to distinguish the different species. The genetic similarity matrix (GSM) revealed variability among the accessions ranging from 0.116 to 0.816. The intraspecific GSM for Z. schinifolium and Z. piperitum was 0.177–0.780 and 0.250–0.816, respectively. The GSM findings indicate that Z. schinifolium and Z. piperitum accessions have high genetic diversity and possess germplasms qualifying as good genetic resources for cross breeding. The clustering analysis separated Z. schinifolium and Z. piperitum into independent groups, and all accessions could be classified into three categories. Z. Schinifolium var. nermis belonged to independent groups. Comparison of the clusters based on morphological analysis with those based on ISSR data resulted in an unclear pattern of division among the accessions. The study findings indicate that Z. schinifolium and Z. piperitum accessions have genetic diversity, and ISSR markers were useful for identifying Z. schinifolium and Z. piperitum.

Background : Codonopsis lanceolata is a flowering perennial climber. The roots are used as medicinal materials or vegetables. C. lanceolata is distributed in India and East Asia such as China, Japan as well as Korea. Recently, demand for C. lanceolata is increasing as a healthy food. In South Korea, this plant is widely cultivated in Gangwon-do province. Although, C. lanceolata is one of the most important medicinal plants in Korea, an elite, inbred line or a variety has not been developed yet. Simple sequence repeat (SSR) marker is a powerful tool for analysis of genetic relationships. In addition, it is a useful tool for studying the non-reference plant genome, due to its even distribution throughout the genome, as well as its high polymorphism between individuals. Methods and Results : We constructed microsatellite-enrichment libraries using C. lanceolata genomic DNA, and obtained a total of 226 non-redundant contig sequences. Routine PCR was performed using gDNA as templates for the polymorphic markers screening. Finally, total 15 polymorphic SSR markers based on C. lanceolata genomic sequences were successfully developed. These markers were applied to 53 C. lanceolata collected from Korea. 103 alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. The average of observed heterozygosity and genetic diversity were 0.42 and 0.62, respectively. The average of polymorphism information content (PIC) value was 0.57. The genetic distance value ranged from 0.73 to 0.93, and there was no observed distinct group according to the collecting areas. Conclusion : We developed 15 novel SSR markers from C. lanceolata genomic sequences for further genetic studies. Also, we concluded that the lineage of C. lanceolata collected in Korea has not been established systematically.

Understanding the genetic variation among landrace collections is important for crop improvement and utilization of valuable genetic resources. The present study was carried out to analyse the genetic diversity and associated population structure of 621 foxtail millet accessions of Korean landraces using 22 EST-SSR markers. A total of 121 alleles were detected from all accessions with an average of 5.5 alleles per microsatellite locus. The average values of gene diversity, polymorphism information content, and expected heterozygosity were 0.518, 0.594, and 0.034, respectively. Following the unweighted neighbor-joining method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 3 clusters, and population structure analysis also separated into 3 populations. Principal coordinate analysis (PCoA) explained a variation of 13.88% and 10.99% by first and second coordinates, respectively. However, in PCoA analysis, clear population-level clusters could not be found. This pattern of distribution might be the result of gene flow via germplasm exchanges in nearby regions. The results indicate that these Korean landraces of foxtail millet exhibit a moderate level of diversity. This study demonstrated that molecular marker strategies could contribute to a better understanding of the genetic structure in foxtail millet germplasm, and provides potentially useful information for developing conservation and breeding strategies.

Background : Wild-cultivated P. ginseng (WCG) is a specific ginseng in Korea which depends on artificial forest growth method. To obtain a WCG which is similar to wild ginseng (WG), this method usually performed in a mountain using seeds or seedlings of cultivated ginseng (CG) and WG. Recently, very high price of WCG caused the problem that Panax notoginseng or Panax quinquefolium are sold as WCG in Korean market. This is concerned as a serious problem to consumers. In this study, we tried to develop a method to discriminate WCG, CG or WG using simple sequence repeat (SSR) markers and phylogenetic analysis. Methods and Results : WCG samples (3, 5, or 6-years old) were collected in Hoengseong, Gangwondo. DNA extraction was performed using CTAB method. SSR markers were collected from the published papers. After test PCR using the markers, one of the primer pair was labeled with fluorescence dye (FAM, NED, PET, or VIC) and Gene Scan analysis were performed. NTsys-PC program was used for the phylogenetic analysis of the data. Eight SSR markers were collected from the published literature and used for the analysis. From the 8 tested SSR markers, 7 SSR markers showed polymorphism between varieties. GenScan analysis were performed using the selected SSR markers to analyze the phylogenetic relationship of WCG. Conclusion : Phylogenetic analysis showed the relationship between WCG and P. ginseng cultivars and the seven SSR markers used in this study are able to distinguish Wild-cultivated P. ginseng.

Background : Codonopsis is a flowering plants belong to the family Campanulaceae, and has many kinds of medicinal properties. As currently recognized, two other groups, Campanumoea and Leptocodon, are included in the Codonopsis. The enlarged genus Codonopsis is distributed in Eastern, Southern, Central, and Southeastern Asia. C. lanceolata, C. clematidea and C. pilosula has many kinds of medicinal properties and this plants are used as medicinal and edible plants. C. ovata and C. mollis are distributed in Pakistan Kashmir and Himalaya mountains at an altitude of about 3,000 m, and flowers bloom in July to August. Methods and Results : In this study, we analyzed the genetic diversity of 5 Codonopsis species using 8 SSR markers base on C. lancelolata genomic sequences. Samples were obtained from fresh leaves of 5 plants from each species and genomic DNA was extracted using CTAB method. PCR was performed in total 20μl reaction volume containing 20 ng of DNA template and 5 pmole of primers. PCR conditions composed pre-denaturation at 95℃ for 5 min, then 35 cycles of 95°C for 30 sec, 60°C for 30 sec and 72°C for 30 sec, and a final extension at 72℃ for 30 min. The amplified band sizes ranged from 74 to 301 bp and clearly showed single or doble bands in eletrophoresis. From the phylogenetic analysis, C. lanceolata was grouped together, but the others were not grouped together according to the species. Conclusion : We concluded that C. lanceolata cultivated in Korea is different from the other species, and the eight SSR markers used in this study are able to distinguish C. lanceolata from the other species.

Plant breeding requires the collection of genetically diverse genetic resources. Studies on the characteristics of Platycodon grandiflorum resources have not been carried out so far. The present study was carried out to discriminate P. grandiflorum based on morphological characteristics and genetic diversity using simple sequence repeat (SSR) markers. Methods and Results :We collected 11 P. grandiflorum cultivars: Maries II, Hakone double white, Hakone double blue, Fuji white, Fuji pink, Fuji blue, Astra white, Astra pink, Astra blue, Astra semi-double blue and Jangbaek. Analyses of the morphological characteristics of the collection were conducted for aerial parts (flower, stem and leaf) and underground parts (root). Next, the genetic diversity of all P. grandiflorum resources was analyzed using SSR markers employing the DNA fragment analysis method. We determined that the 11 P. grandiflorum cultivars analyzed could be classified by plant length, leaf number and root characteristic. Based on the genetic diversity analysis, these cultivars were classified into four distinct groups. Conclusions : These findings could be used for further research on cultivar development using molecular breeding techniques and for conservation of the genetic diversity of P. grandiflorum. Moreover, the markers could be used for genetic mapping of the plant and marker-assisted selection for crop breeding.

Lonicera caerulea var. edulis is a rare species found in some alpine region of Korea. Genetic variation in L. caerulea var. edulis has been investigated by examining 161 individuals from six natural populations: Mt. Seorak 1, Mt. Seorak 2, Mt. Jeombong, Mt. Bangtae, Mt. Gyebang, Mt. Halla. The mean genetic diversity for all the six populations was 0.25 (S.I.). The highest genetic diversity was found in Mt. Seorak (S.I.=0.3158) and the lowest was in Mt. Gyebang (S.I.=0.1047). Comparatively low level of genetic diversity was observed (Ae=1.25, P= 64.6%, S.I.=0.25), which is a typical pattern for rare tree species. AMOVA showed exceptionally large proportion of genetic variations both for among populations (34.69%) and within populations (65.31%). Excluding Mt. Gyebang, the genetic variation among and within population was 18.71% and 81.29% respectively. The UPGMA dendrogram based on genetic distance is not suitable for geographic relationship. Genetic distance of Mt. Gyebang was most distant from the other populations. Excluding Mt. Gyebang, the genetic identities among the five populations were 0.95 to 0.97, which is very high similarity level of genetic identity. This low level of genetic variations and the lack of site in nature indicates that L. caerulea var. edulis demanded a serious conservation.

In this study, genetic diversity of wild Codonopsis lanceolata collected in Korea were analysed using SSR makers. Wild C. lanceolata roots were collected in Jeollanam-do Jangheung-gun Choentae Mountain as in roots. The wild C. lanceolata plants were cultivated in Chungbuk National University greenhouse and the leaves were sampled from 36 plants. The genomic DNA of C. lanceolata was extracted using CTAB. PCR was performed using a program of 35 cycles at 94℃ for 30 sec, 60℃ for 30 sec, and 72℃ for 30 sec with an pre-denaturation of 94℃ for 5 min and a final extension of 72℃ for 30 min. The PCR reaction mixture contains 5 pmole of primers and 20 ng of DNA template in a 20 μL reaction volume. The genotype of the analyzed samples were very different. Therefore, the wild C. lanceolata collected in Korea look genetically diverse.

Codonopsis lanceolata is a perennial climber. The roots are used as medicinal materials or vegetables. Recently, demand for C. lanceolata is increasing as a healthy food. C. lanceolata is distributed in India and East Asia such as China, Japan as well as Korea. In South Korea, this plant is widely cultivated in Gangwon-do province. No C. lanceolata varieties were developed in Korea. The objective of this study is to analyze genetic diversity of C. lanceolata cultivated in Korea using SSR makers. C. lanceolata roots were collected in each region were cultivated in Chungbuk National University greenhouse. Samples were obtained from fresh leaves of 5 plants from each collection region. The genomic DNA was extracted using CTAB. Genetic diversity was analysed using 4 sets of C. lanceolata SSR makers. PCR was performed in total 20 μL reaction volume containing 20 ng of DNA template, 5 pmole of primers. The genotypes of the analyzed samples were very similar. That means that the genetic diversity of C. lanceolata cultivated in Korea is very low.

Pepper (Capsicum spp.) germplasm shows diverse phenotypic variations including fruit size, color, pungency, and many other horticultural traits. Traditional markers including SSR, AFLP, and RFLP have been used to construct genetic maps using biparental populations. However to assess the genetic diversity of large number of germplasm, a robust and rapid marker development and genotyping approach is needed. We used six pepper accessions including C. annuum, C. chinense, C. baccatum and C. frutescens and performed genotyping-by-sequencing (GBS). To select the most appropriate condition, eight different 2 bp selective nucleotides were used to make GBS libraries. Selective nucleotide ‘OO’ showed the largest number of reads in all samples, and 11,026 to 47,957 high-quality SNPs were called in six accessions. When C. annuum ‘CM334’ genome sequence was used as a reference, C. annuum showed the smallest number of SNPs, while C. baccatum which was known to be a different Capsicum clade showed the largest number of SNPs. Pepper core collection chosen to represent the genetic diversity of whole germplasm will be genotyped by high-density SNPs developed from GBS. We will perform genome-wide association study (GWAS) using genetic and phenotypic variation to identify the functional genetic loci controlling horticultural traits.

Chrysanthemum (Chrysanthemum morifolium) is one of the most popular ornamental species in the world due to the great diversity of inflorescence form and color. There has been increasing demands for various types of chrysanthemums, such as cut flowers, potted plants and bedding plants. However, the genomic studies of this species have been not extensively conducted relative to other ornamental species due to high levels of polyploidy (2n = 4x =36 or 2n = 6x = 54) and heterozygosity as well as large genome size. In this work, we developed a molecular tool for cultivar identification using simple sequence repeats (SSRs) and investigated genetic diversity in 127 chrysanthemum cultivars. Of the 150 SSR primer pairs tested in this study, 62 primers were obtained from previous studies, while 88 primers were designed using the unigene sequences of C. nankingense and the Expressed Sequence Tag (EST) sequences of C. morifolium in the NCBI database. Thirty SSR primers were selected based on polymorphism and banding patterns in a subset of 8 cultivars and used to amplify the DNA of 127 chrysanthemum cultivars. The UPGMA dendrogram based on these 30 SSR markers showed that most of chrysanthemum cultivars were divided into five clusters. These results will benefit chrysanthemum research community to develop elite cultivars.

Assessing genetic diversity, population structure, and linkage disequilibrium is important in identifying potential parental lines for breeding programs. In this study, we assessed the genetic and phenotypic variation of 174 normal maize (Zea mays) inbred lines and made association analyses with respect to nine agronomical traits, using 150 simple sequence repeats (SSR). From population structure analysis, the lines were divided into three groups. Association analysis was done with a mixed linear model and a general linear model. Twenty one marker-trait associations involving 19 SSR markers were observed using the mixed model, with a significance level of P<0.01. All of these associations, as well as 120 additional marker-trait associations involving 77 SSR markers, were observed with the general model. Two significant marker-trait associations (SMTAs) were detected at P ≤ 0.0001. In the mixed linear model, one locus was associated with water content, two loci were associated with 100-kernel weight, setted ear length, ear thickness and stem thickness; three loci were associated with ear height, four loci were associated with total kernel weight and five loci were associated with plant height. These results should prove useful to breeders in the selection of parental lines and markers.

In this study we evaluate the informative and efficiency of Simple Sequence Repeat (SSR) and Sequence Specific Amplified Polymorphism (SSAP) markers for genetic diversity, genetic relationship and population structure among 87 super sweet corn inbred lines generated by different origins. The SSR showed relatively higher level of the average gene diversity and shannon’s information index value than that of the SSAP. To assess genetic relationship and to characterize among 87 super sweet corn inbred lines using the SSR and SSAP markers. The dendrogram using SSR marker divided into nine groups of clusters were observed at the genetic similarity value 53.0%. For SSAP marker, Total three main clusters were confirmed in genetic similarity value at 50.8%. Result of combine data for SSR and SSAP markers showed six subgroup were detected in genetic similarity at 53.5%. To confirm population structure, the total 87 super sweet corn inbred lines were divided into groups I, II and admixed group based on membership probability 0.8 for SSR and SSAP markers. However population structure using combine data was K=3 and divided into group I, II, III and admixed group. This study has demonstrated the comparative analysis of SSR and SSAP for the study of genetic diversity and the genetic relationship for super sweet corn inbred lines. Thus, the results of this study will be useful to maize breeding programs in Korea.

For understanding the genetic diversity and genetic relationship between cultivated and weedy types, we evaluated genetic variation of 80 accessions of rice (O. Sativa). This included 42 cultivated accessions and 38 weedy accessions with the help of AFLP and CACTA-TD. A total of 542 loci were analyzed (255 for AFLP and 287 for CACTA-TD) of which AFLP markers exhibited 75% of polymorphism and transposon based CACTA-TD markers exhibited 93% of polymorphism. The average genetic diversity value for all 80 accessions, using AFLP markers was 0.226 (Cultivated – 0.210; Weedy 0.241) and based on CACTA-TD markers was 0.281 (Cultivated – 0.294; Weedy 0.269). A UPGMA phylogenetic tree revealed three major groups for both the marker system. The average polymorphic content value obtained with AFLP and CACTA-TD markers were 0.21 and 0.232, Effective multiplex ratio (AFLP – 47.50; CACTA-TD – 66.75), Marker Index (AFLP – 9.94; CACTA-TD – 21.13) and Resolving power (AFLP – 19.53; CACTA-TD – 34.62) indicated that the CACTA-TD markers were relatively efficient than AFLP markers.

Glutenin is the major factor responsible for the unique viscoelastic dough characterisitcs of wheat flour, which determine mixing and bread baking performance(X.Shan et al, 2007). And early maturity is one of the most important cultural characteristic in Korea because of its winter cropping system. This study is to reveal the genetic properties of Asian wheat landrace collection originated from 6 separate regions such as Korea, China, Japan, Afganistan, Iran, Pakistan, Caucasus, and Middle East. Using germplasms maintained in National Agrobiodiversity Center, RDA, Korea, the variations in morphological character and HMW glutenin subunit composition were investigated. In this study, Glu-A1c(null), Glu-B1b(7+8) and Glu-D1a(2+12) alleles are the most frequent in Asian landrace wheats. When it comes to unique composition, Glu-B1aj(8) and Glu-D1q(2+11) subunits are only in Afghanistan wheat. And Glu-B1k(22), Glu-D1l(12), Glu-D1m(10) subunits are only in accessions from Pakistan, Korea, and China, respectively. The accessions from Iran and Caucasus have the highest PIC value(0.57), which shows wheat origin region has high genetic diversity. Grouping by UPGMA anlysis of combination of Glu-1 allele, most accessions from Afghanistan, Korea, and Japan were in the same group despite of geological distance. Contrasively, many germplasms originated from China, Caucasus, and Middle East were in the other same group. The evaluation of bread baking quality by Glu-1 scoring system, 34 accessions are perfect 10. 16 samples from China and 1 Afghanistan among them were also matured before early June, suitable to Korean cropping system. Especially, 3 accessions(K151847, K151865, K151962) had extremely early maturity, ripened before late May. These genetic resources having good gluten quality and early maturity are expected to be used for Korea wheat breeding system.

Radish (Raphanus sativus L.) is a widely-consumed root vegetable that is grown worldwide. To utilize the radish genetic resources for breeding research, we collected radish germplasms and evaluated their morphological and genetical characteristics. Here, phylogenetic relationship of 288 accessions were analyzed using 16 SSR markers and classified cytoplasm male sterility (CMS) types using cpDNA-based molecular markers. To create a collection of 288 accessions, 188 and 73 accessions were selected from RDA-Genebank (Korea) and NIAS-Genebank (Japan), respectively, after generation advancement for the accessions with low uniformity. In addition, 27 elite lines currently used for commercial radish breeding programs were included. In the result of phylogenetic analysis, 288 accessions were clustered into 5 major groups corresponding to the morphological traits and origins at the similarity coefficient value of 0.51. Analysis of CMS types revealed that majority of accessions were determined as DBRMF1 and DBRMF2 mitotypes, 15 accessions to Ogura and 4 accessions to DCGMS mitotypes. Further genetic analysis for radish germplasm will be valuable in assisting radish f1 hybrid breeding.