• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.1
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• pp.69-72
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• 2004

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.5
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• pp.429-433
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• 2004

A single recessive gene, rxp, controls the bacterial leaf pustule (BLP) resistance in soybean and in our previous article, it has been mapped on linkage group (LG) D2 of molecular genetic map of soybean. A total of 130 recombinant inbred lines (RILs) from a cross between BLP-resistant SS2-2 and BLP-susceptible Jangyeobkong were used to identify molecular markers linked to rxp. Fifteen simple sequence repeat (SSR) markers on LG D2 were screened to construct a genetic map of rxp locus. Only four SSR markers, Satt135, Satt372, Satt448, and Satt486, showed parental polymorphisms. Using these markers, genetic scaffold map was constructed covering 26.2cM. Based on the single analysis of variance, Satt372 among these four SSR markers was the most significantly associated with the resistance to BLP. To develop new amplified fragment length polymorphism (AFLP) marker linked to the resistance gene, bulked segregant analysis (BSA) was employed. Resistance and susceptible bulks were made by pooling equal amount of genomic DNAs from ten of each in the segregating population. A total of 192 primer combinations were used to identify specific bands to the resistance, selecting three putative AFLP markers. These AFLP markers produced the fragment present in SS2-2 and the resistant bulk, and not in Jangyeobkong and the susceptible bulk. Linkage analysis revealed that McctEact97 $(P=0.0004,\;R^2=14.67\%)$ was more significant than Satt372, previously reported as the most closely linked marker.

• Mycobiology
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• v.47 no.4
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• pp.527-532
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• 2019

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (M_AF) and the average number of alleles (N_A) were 0.50 and 5.47, respectively. The average number of genotypes (N_G), observed heterozygosity (H_O), expected heterozygosity (H_E), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson's correlation coefficient showed that M_AF was negatively correlated with N_G (-0.683), N_A (-0.600), H_O (-0.584), and PIC (-0.941). N_G, N_A, H_O, and PIC were positively correlated with other polymorphic parameters except for M_AF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

• 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.31 no.3
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• pp.337-343
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• 2013

The aims of this study were to compare genetic distances among 14 Phalaenopsis varieties using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) marker systems and to determine the discrimination using SSR. A total of 111 SSR primers and 30 SRAP combinations were initially screened. Twelve SSR primers and thirty SRAP combinations showed high polymorphism among the 14 Phalaenopsis varieties including domestic breeding varieties, conserved in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected by silver staining method. A total of 474 polymorphic bands, including 55 by SSRs and 419 by SRAPs, were identified and used for genetic diversity analysis. Polymorphic bands were scored for calculating a simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. Fourteen Phalaenopsis varieties were classified into three major groups at similarity coefficient value of 0.683 and 0.66 using SRAP and SSR, respectively. Also we could discriminate these domestic breeding Palaenopsis varieties using only SSR 20 and SSR 22. The results indicate that SSR analysis is effective for discrimination among Phalaenopsis varieties and SRAP is useful for genetic diversity when there is no sequence information. These studied SSR and SRAP markers will be useful tools for genotype identification, germplasm conservation and genetic relationship study in Phalaenopsis.

• Mycobiology
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• v.47 no.4
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• pp.466-472
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• 2019

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.11-22
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• 2010

The population structure of a domesticated species is influenced by the natural history of the populations of its pre-domesticated ancestors, as well as by the breeding system and complexity of breeding practices implemented by humans. In the genetic and population structure analysis of 122 South Asia collections using 29 simple sequence repeat (SSR) markers, 362 alleles were detected, with an average of 12.5 per locus. The average expected heterozygosity and polymorphism information content (PIC) for each SSR locus were 0.74 and 0.72,respectively. The model-based structure analysis revealed the presence of three clusters with the 91.8% (shared > 75%) membership, with 8.2% showing admixture. The genetic distances of Clusters 1-3 were 0.55, 0.56, and 0.68, respectively. Polymorphic information content followed the same trend (Cluster 3 had the highest value and Cluster 1 had smallest value), with genetic distances for each cluster of 0.52, 0.52, and 0.65, respectively. This result could be used for supporting rice breeding programs in South Asia countries.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.48 no.1
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• pp.56-64
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• 2003

If a quantitative trait loci (QTL) marker identified in a population is applicable to different populations (marker universality), this will not only reduce the labor and cost in marker assisted selection (MAS), but accelerate the application of molecular markers to real breeding programs. Present study aims to evaluate the defined QTL related markers from a population to a different breeding population for the MAS. Four rice breeding populations were subjected to seventy-five simple sequence repeat (SSR) markers which were already identified for their polymorphism information content (PIC) in the parents of the crossings. Among them, eight markers were evaluated for their correlation between presence of marker alleles and phenotypic expression in breeding populations. A reasonable level of polymorphism for the mapped markers originated from any sources of rice accessions was observed between crosses of any sources (marker repeatability). However, correlation between presence of markers and expression of the traits in rice breeding populations was not significant except for minor portion of traits and markers examined (failure of marker universality). In the present study, various strategies were discussed to develop new markers with universality of breeding application.

• Mycobiology
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• v.46 no.4
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• pp.421-428
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• 2018

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

• Korean Journal of Plant Taxonomy
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• v.48 no.3
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• pp.195-200
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• 2018

Genetic assessments of rare and endangered species are among the first steps necessary to establish the proper management of natural populations. Transcriptome-derived single-sequence repeat markers were developed for the Korean endangered species Astilboides tabularis (Saxifragaceae) to assess its genetic diversity. A total of 96 candidate microsatellite loci were isolated based on transcriptome data using Illumina pair end sequencing. Of these, 26 were polymorphic, with one to five alleles per locus in 60 individuals from three populations of A. tabularis. The observed and expected heterozygosity per locus ranged from 0.000 to 0.950 and from 0.000 to 0.741, respectively. These polymorphic transcriptome-derived simple sequence repeat markers would be invaluable for future studies of population genetics and for ecological conservation of the endangered species A. tabularis.