Bulb onion (Allium cepa), which belongs to the family Amaryllidaceae, is one of the oldest vegetative crops known to humans. Despite its high economic value, only a few reports are available on the use of molecular markers in genetic diversity analysis of Allium cepa for its improvement. Molecular genetic markers have been widely used as powerful tools for analyzing the plant genome. In particular, Microsatellites or simple sequence repeats (SSRs) markers are tandem repeats of one to six bp in length and have been proven to be the most powerful polymerase chain reaction (PCR)-based DNA markers in plant diversity analysis. In this study, the genomic DNA was isolated from different Allium cepa lines. The ESTs and gDNA sequences of onion were collected from National Center for Biotechnology information. The SSRs with two to five motifs over a length of 12 bp, were identified using SSRIT (Gramene) software. The PCR products of 100 to 350 bp in length containing SSRs, primers was designed using Primer3 with lengths of 20 to 24 bp and a melting temperature of 60℃. The SSR markers with high polymorphism-information content (PIC) levels was useful for collecting progeny with high genetic homogeneity for onion breeding, and to obtain representative marker sets for genetic tests. The SSR Finder program and the developed SSR markers could be a useful resource for genetic diversity and purity testing in onion.

Ramie (Boehmeria nivea L. Gaudich.) is a hardy perennial herbaceous plant of the Urticaceae family and has been grown as a fiber crop in several countries including Korea for many centuries. Ramie leaves also have been traditionally used as a major ingredient of a type of rice cake called ‘Song-pyun’ in the Southwest area of Korea, especially Yeong-Gwang province. Despite its economic importance, the molecular genetics of ramie have not been studied in detail yet. Genetic resources of ramie were widely collected from domestic local sites by Bioenergy Crop Research Center (RDA) and Yeong-Gwang Agricultural Technology Center. For the systematic and efficient management of the genetic resources, we developed microsatellite molecular markers of ramie. To do this, we generated microsatellite-enriched genomic DNA libraries using magnetic bead hybridization selection method. 216 contigs containing microsatellite repeat motif were generated using nucleotide sequences of 376 clones from the libraries. Primer sets were designed from the flanking sequences of the repeat motif. Finally, we selected 26 microsatellite markers, possibly showing polymorphism among the genetic resources. Results on the genotype analysis of the ramie genetic resources using the microsatellite markers will be presented.

Rice genetic resources are composed of various species and ecotypes, and each accession reveals different genetic and phenotypic characters. For the managenment of diverse rice genetic resources, seed integrity is important factor in that the individuals of one accession in self-pollinating crop might be homogeneous. To elevate the management efficiency of rice germplasm contrary to the phenotypic distinction, we focused on applicable microsatellite markers because this markers are widly used for genetic evaluation in diverse genetic resources with a character of high reproducibility and polymorphism. In this regard, we selected microsatellite markers based on genotypes; diversity set including 150 accessions using 249 SSR markers. As SSR loci with high PIC(polymorphism information content) values usually revealed multi bands in one accession, proper genotyping were difficult in these loci. Therefor, we checked the band clarity in addition to PIC values and chose 12 and 6 SSR markers finally. All accessions of rice diversity set were distinguished with the first marker set comprising 12 SSR markers, and only 3 combinations of tested accessions(0.03%, 3/11,175) showed same genotype with second marker set comprising 6 SSR markers. The tested 142 Korean bred varieties revealed 0.19%(19/10,011 combinations) and 0.69%(69/10,011 combinations) genotypic identity using first and second marker set, respectively. These newly selected markers might be useful for the analysis of genetic homogeneity and relationship in rice genetic resources.

Microsatellites are one of the most suitable markers for variety identification as it has great discrimination power for varieties with narrow genetic variation. The polymorphism level between forty microsatellite primer pairs and 148 soybean varieties was investigated through fluorescence based automatic detection system. A set of 16 primer pairs showed highly reproducible and polymorphic in these varieties. A total of 204 alleles were detected by using 16 microsatellite markers. The number of alleles per locus ranged from 6 to 28 with an average of 12.75 alleles per locus. The average polymorphism information content (PIC) was 0.86 ranging from 0.75 to 0.95. Two hundred four microsatellite loci were used to calculate Jaccard’s distance coefficients for unweighted pair group method using the arithmetic averages cluster analysis. These varieties were separated into several distinctive groups corresponding to varietal types. All of the varieties were perfectively discriminated by markers genotypes. This information may be useful to compare through genetic relationship analysis between existing and candidate varieties in distinctive tests and protection of plant breeders’ intellectual properties rights through variety identification.

Microsatellite is one of the most suitable markers for variety identification as it has great discrimination power for varieties with narrow genetic variation. The relationship between marker genotypes and 58 melon varieties was analyzed. Of the 400 pairs of simple sequence repeat (SSR) primers screened against 11 melon varieties. 28 pairs showed highly polymorphism on the basis of PIC (Polymorphism Information Contents) value. These markers were applied to constructing DNA profile data base of 58 major melon varieties through multiplex PCR and fluorescence based automatic detection system. A total of 111 polymorphic amplified fragments were obtained by using 28 SSR markers. The average of PIC value was 0.643 ranging from 0.401 to 0.846. One hundred eleven SSR loci were used to calculate Jaccard’s distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of SSR analysis, were categorized into plant shape and fruit type. Almost all of the varieties were discriminated by marker genotypes. This information may be used to select comparative variety through comparison of genetic relationship between existing variety and candidate varieties in distinctive tests and protection of plant breeders’ intellectual property rights through variety identification.

Microsatellite marker is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. The suitability of simple sequence repeat (SSR) markers for varietal identification and genetic diversity were evaluated for 325 rice varieties. Four hundred thirty six pairs of SSR primers were screened against 11 rice varieties. Twenty six primer pairs were highly polymorphic and reproducible. These primer sets were used to construct a DNA profile database containing 325 rice varieties grown in Korea through automatic detection system (ABI 3130XL). Microsatellite polymorphism was showed to be high. A total of 331 polymorphic amplified fragments were obtained by using 26 microsatellite markers. The number of alleles per locus ranged from 9 to 18 with an average of 12.73 alleles per locus. The average polymorphism information content (PIC) was 0.734 ranging from 0.555 to 0.880. Three hundred thirty one SSR loci were used to calculate Jaccard’s distance coefficients for UPGMA cluster analysis. These varieties were separated into several distinctive groups corresponding to varietal types. Almost all of the varieties were discriminated by SSR marker genotypes. This information may be useful to select comparative variety through comparison of genetic relationship analysis between existing variety and candidate varieties in distinctive tests.

The present study reports isolation and characterization of ten polymorphic SSR markers developed from common buckwheat (Fagopyrum esculentum Moench). These SSR markers produced a total of 59 alleles across 41 common buckwheat accessions with an average of 5.9 alleles per locus. Values for observed (HO) and expected (HE) heterozygosities ranged from 0.071 to 0.924 (mean=0.53) and from 0.073 to 0.902 (mean=0.412), respectively. At significance threshold (P<0.05), seven loci deviated from Hardy-Weinberg equilibrium (HWE), whereas significant linkage disequilibrium (LD) values were observed between 5 pairs of loci. These markers are currently being used for programming of the genetic conservation and classification of common buckwheat germplasm collection.

Knowledge of genetic diversity and of the genetic relationships among elite breeding materials has had a significant impact on the improvement of crops. In maize, this information is particularly useful in i) planning crosses for hybrid and line development, ii) in assigning lines to heterotic groups and iii) in plant variety protection. We have used the SSR technique to study the genetic diversity and genetic relationships among 76 Korean waxy corn accessions, representing a diverse collection from throughout Korea. Assessment of genetic diversity among members of this group was conducted using 30 microsatellite markers. Among these 30 microsatellite markers, we identified a total of 127 alleles (with an average of 4.2 and a range of between 2 and 9 alleles per locus). Gene diversity at these 30 microsatellite loci varied from 0.125 to 0.795 with an average of 0.507. The cluster tree generated with the described microsatellite markers recognized two major groups with 36.5% genetic similarity. Group I includes 63 inbred lines, with similarity coefficients of between 0.365 and 0.99. Group II includes 13 inbred lines, with similarity coefficients of between 0.45 and 0.85. The present study indicates that the 30 microsatellite loci chosen for this analysis are effective molecular markers for the assessment of genetic diversity and genetic relationships between Korean waxy corn accessions. Specifically, this study's assessment of genetic diversity and relationships between a set of 76 Korean waxy corn inbred lines will be helpful for such activities as planning crosses for hybrid and line development and association mapping analyses of maize breeding programs in Korea.

Genetic diversity and relationship among the accessions of cultivated types of Perilla frutescens and their weedy types were studied with 11 microsatellite markers. A total of 101 alleles were detected with an average allele number of 9.2 per locus among 70 Perilla accessions. Number of alleles per locus ranged from two for KWPE-39 to 21 for KWPE-53 and gene diversity for each locus was varied from 0.479 to 0.918 with an average of 0.715. The average gene diversity value was 0.626, 0.657, 0.509 and 0.524 for cultivated and weedy types of var. frutescens, and cultivated and weedy types of var. crispa, respectively. The weedy type accessions of var. frutescens and var. crispa showed more variation than corresponding cultivated type accessions. As for the cultivated type of var. frutescens, the accessions from China showed higher microsatellite diversity than those of Korea and Japan. An UPGMA phylogenetic tree revealed three major groups which were congruent with their morphological characters and geographical distribution patterns except for a few odd accessions. Although the wild ancestral species of cultivated types of P. frutescens has not yet been identified, our results may provide some evidence for the origin and the diffusion route of cultivated type of var. frutescens in East Asia. Cultivated Perilla crop might be originated in China, and its diffusion might be from China to Japan via Korea and the weedy types of Perilla crop are the key taxon in understanding the origin of cultivated type of both var. frutescens and of var. crispa.