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

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.5
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• pp.416-419
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• 2001

Hypernodulation soybean mutant, SS2-2, is characterized with greater nodulation and nitrogen fixing ability in the root nodule than its wild type, Shinpaldalkong 2. The present study was performed to identify a genetic locus conferring hypernodulation in soybean mutant SS2-2 and to determine whether the gene controlling the hypernodulation of SS2-2 is allelic to that controlling the supernodulation of nts382 mutant. Hybridization studies between SS2-2 and Taekwangkong revealed that the recessive gene was responsible for the hypernodulation character in soybean mutant SS2-2. Allelism was also tested by crossing supernodulating mutant nts382 and hypernodulating mutant SS2-2 that both hypernodulation and supernodulation genes were likely controlled by an identical locus. Molecular marker mapping of hypernodulation gene in SS2-2 using SSR markers confirmed that the gene conferring hypernodulation was located at the same loci with the gene conferring supernodulation. It is interesting to note that the same gene controlled the super- and hyper-nodulation characters, although SS2-2 and nts 382 exhibited differences in the amount of nodulation in the root system. Further genetic studies should be needed to clarify the genetic regulation of super- and hyper-nodulation in soybean.

• Korean Journal of Plant Resources
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• v.29 no.3
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• pp.322-330
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• 2016

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.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.92-92
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• 2017

Bakanae disease is one of the most serious and oldest problems of rice production, which was first described in 1828 in Japan. This disease has also been identified in Asia, Africa, North America, and Italy. Germinating rice seeds in seed boxes for mechanical transplantation has caused many problems associated with diseases, including bakanae disease. Bakanae disease has become a serious problem in the breeding of hybrid rice, which involves the increased use of raising plants in seed beds. The indica rice variety Shingwang was selected as resistant donor to bakanae disease. One hundred sixty nine NILs, YR28297 ($BC_6F_4$) generated by five backcrosses of Shingwang with the genetic background of susceptible japonica variety, Ilpum were used for QTL analysis. Rice bakanae disease pathogen, CF283, was mainly used in this study and inoculation and evaluation of bakanae disease was performed with the method of the large-scale screening method developed by Kim et al. (2014). SSR markers evenly distributed in the entire rice chromosomes were selected from the Gramene database (http://www.gramene.org), and the polymorphic markers were used for frame mapping of a $BC_5F_5$ resistant line. Here, we developed 168 near-isogenic rice lines (NILs, $BC_6F_4$) to locate a QTL for resistance against bakanae disease. The lines were derived from a cross between Shingwang, a highly resistant variety (indica), and Ilpum, a highly susceptible variety (japonica). The 24 markers representing the Shingwang allele in a bakanae disease-resistant NIL, YR24982-9-1 (parental line of the $BC_6F_4$ NILs), were located on chromosome 1, 2, 7, 8, 10, 11, and 12. Single marker analysis using an SSR marker, RM9, showed that a major QTL was located on chromosome 1. The QTL explained 65 % of the total phenotype variation in $BC_6F_4$ NILs. The major QTL designated qBK1 was mapped in 91 kb region between InDel15 and InDel21. The identification of qBK1 and the closely linked SSR marker, InDel18, could be useful for improving rice bakanae disease resistance in marker-assisted breeding.

• The Plant Pathology Journal
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• v.19 no.1
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• pp.24-29
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• 2003

SS2-2, a hypernodulating soybean mutant was isolated by EMS mutagenesis from Sinpaldalkong 2. This auto-regulation mutant showed greater number of nodules and smaller plant size than its wild type Sinpaldalkong 2. SSR markers were used to identify DNA variation at SSR loci from different soybean LG. The only SSR marker that detected a length polymorphism between SS2-2 and its wild type ancestor was Satt294 on LG C1 instead of LG H, locating a hypernodulating gene. Sequencing data of flanking Satt294 indicated that the size variation was due to extra stretch of TTA repeats of the SSR motif in SS2-2, along with $A\longrightarrow$G transversion. In spite of phenotypic differences between the wild type and its hypernodulating mutants, genomic DNA poly-morphisms at microsatellite loci could not control regulation of nodule formation. The cDNA-AFLP method was applied to compare differential display of cDNA between Sinpaldalkong 2 and SS2-2. After isolation and sequence comparison with many AELP fragments, several interesting genes were identified. Northern blot analysis, immunolocalization and/or the yeast two-hybrid system with these genes might provide information on regulation of nodule development in SS2-2.

• Korean Journal of Medicinal Crop Science
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• v.25 no.6
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• pp.411-417
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• 2017

Background: Adenophora triphylla var. japonica (Regel) H. Hara shows vegetative growth with radical leaves during the first year and shows reproductive growth with cauline leaves and bolting during the second year. In addition, the shape of the plant varies within the same species. For this reason, there are limitations to classifying the species by visual examination. However, there is not sufficient genetic information or molecular tools to analyze the genetic diversity of the plant. Methods and Results: Approximately 34.59 Gbp of raw data containing 342,487,502 reads was obtained from next generation sequencing (NGS) and these reads were assembled into 357,211 scaffolds. A total of 84,106 simple sequence repeat (SSR) regions were identified and 14,133 primer sets were designed. From the designed primer sets, 95 were randomly selected and were applied to the genomic DNA which was extracted from five plants and pooled. Thirty-nine primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis. Conclusions: The 39 novel SSR markers developed in this study could be used for the genetic diversity analysis, variety identification, new variety development and molecular breeding of A. triphylla.

• Plant Breeding and Biotechnology
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• v.5 no.3
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• pp.183-191
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• 2017

Finger millet (Eleusine coracana L. Gaertn.) is an important cereal crop in eastern Africa and southern India with excellent grain storage capacity and the unique ability to thrive in extreme environmental conditions. In this study, we analyzed the genetic diversity and population structure of finger millet using 12 developed microsatellites. By sequencing 815 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in finger millet accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 76 finger millet accessions in Asia, Africa, and unknown origins. The number of alleles ranged from 2 to 9, with an average of 3.3 alleles. The mean values of observed heterozygosity and expected heterozygosity were 0.27 and 0.35, respectively. The average polymorphism information content was 0.301 in all 76 finger millet accessions. AMOVA analysis showed that the percentage of molecular variance among the populations was 1%, that among individuals was 5%, and that within individuals was 94%. In STRUCTURE analysis, the 76 finger millet accessions were divided into two subpopulations which had an admixture of alleles. There was a correspondence among PCoA, AMOVA, and population structure. This study may form the basis for a finger millet breeding and improvement program.

• Genomics & Informatics
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• v.19 no.3
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.45-45
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• 2020

A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of foxtail millet EST-SSRs in barnyard millet. A total of 312 EST-SSRs of foxtail millet were tested using 84 Echinochloa crus-galli germplasm accessions; a high rate of transferability (62%) and 46 primer sets (13%) were shown the polymorphism in barnyard millet. The 13% of functional EST-SSRs) was demonstrated between cereals and barnyard millet. SSR marker profile data were scored for the computation of pairwise distances as well as a Neighbor Joining (NJ) tree of all the genotypes. The averaged values of gene diversity (H_E) and polymorphism information content (PIC) were 0.213 and 0.179 within populations, respectively. The 84 barnyard millet germplasm accessions were divided into five different groups, which agreed well with their geographical origins. The exotic 12 accessions of India type barnyard millet (E. frumentacea) were all separated form Korean local collection genotype. The present results provide evidence of divergence between cultured and wild type barnyard, as a millet and grass. The polymorphic SSR markers indicated in this study were of great value in analysis of genetic diversity that can be further used for crop improvement through breeding.

• The Plant Pathology Journal
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• v.31 no.1
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• pp.12-24
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• 2015

Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1-24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes.