• The Plant Pathology Journal
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• v.36 no.1
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• pp.11-28
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• 2020

Faba bean (Vicia faba L.) is one of the most important legume crops in Egypt. However, production of faba bean is affected by several diseases including fungal diseases. Fusarium wilt incited by Fusarium oxysporum Schlecht. was shown to be the most common wilt disease of faba bean in Assiut Governorate. Evaluation of 16 faba bean genotypes for the resistance to Fusarium wilt was carried out under greenhouse conditions. Three molecular marker systems (inter-simple sequence repeat [ISSR], sequence related amplified polymorphism [SRAP], and simple sequence repeat [SSR]) and a biochemical marker (protein profiles) were used to study the genetic diversity and detect molecular and biochemical markers associated with Fusarium wilt resistance in the tested genotypes. The results showed that certain genotypes of faba bean were resistant to Fusarium wilt, while most of the genotypes were highly susceptible. The percentage of disease severity ranged from 32.83% in Assiut-215 to 64.17% in Misr-3. The genotypes Assiut-215, Roomy-3, Marut-2, and Giza2 were the most resistant, and the genotypes Misr-3, Misr-1, Assiut-143, Giza-40, and Roomy-80 performed as highly susceptible. The genotypes Assiut-215 and Roomy-3 were considered as promising sources of the resistance to Fusarium wilt. SRAP markers showed higher polymorphism (82.53%) compared with SSR (76.85%), ISSR markers (62.24%), and protein profile (31.82%). Specific molecular and biochemical markers associated with Fusarium wilt resistance were identified. The dendrogram based on combined data of molecular and biochemical markers grouped the 16 faba bean genotypes into three clusters. Cluster I included resistant genotypes, cluster II comprised all moderate genotypes and cluster III contained highly susceptible genotypes.

• Journal of Ginseng Research
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• v.35 no.4
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• pp.399-412
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• 2011

Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tagderived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax species and 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an $F_2$ population of a cross between two P. ginseng cultivars, 'Yunpoong' and 'Chunpoong', indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar 'Chunpoong', a subgroup with three accessions including two cultivars, 'Gumpoong' and 'Yunpoong' and one landrace 'Hwangsook' and another subgroup with two accessions including one cultivar, 'Gopoong' and one landrace 'Jakyung'. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure.

• 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.

• Journal of Plant Biotechnology
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• v.46 no.3
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• pp.158-164
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• 2019

Molecular characterization of different genotypes reveals accurate information about the degree of genetic diversity that helps to develop a proper breeding program. In this study, a total of 30 EST-based simple sequence repeat (EST-SSR) markers derived from trumpet lily (Lilium longiflorum) were used across 11 native lily species for their genetic relationship. Among these 30 markers, 24 SSR markers that showed polymorphism were used for evaluation of diversity spectrum. The allelic number at per locus ranged from 1 at SSR2 locus to 34 alleles at SSR15 locus, with an average of 11.25 alleles across 24 loci observed. The polymorphic information content, PIC, values ranged from 0.0523 for SSR9 to 0.9919 for SSR2 in all 24 loci with an average of 0.3827. The allelic frequency at every locus ranged from 0.81% at SSR2 locus to 99.6% at SSR14 locus. The pairwise genetic dissimilarity coefficient revealed the highest genetic distance with a value of 81.7% was in between L. dauricum and L. amabile. A relatively closer genetic distance was found between L. lancifolium and L. dauricum, L. maximowiczii and L. concolor, L. maximowiczii and L. distichum (Jeju), L. tsingtauense and L. callosum, L. cernuum and L. distichum (Jeju ecotype), of which dissimilarity coefficient was 50.0%. The molecular fingerprinting based on microsatellite marker could serve boldly to recognize genetically distant accessions and to sort morphologically close as well as duplicate accessions.

• 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.

• 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.4
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• pp.334-340
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• 2001

Two different types of molecular markers, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), were used to measure genetic diversity among five Korean, eight Thai, and three wild soybeans. For SSR analysis, a total of 20 markers were surveyed to detect polymorphisms. For SNP analysis, four primers were designed from consensus sequence regions on disease resistance protein homolog genes, and used to amplify the genomic region. The PCR products were sequenced. A number of polymorphic SSR and SNP bands were scored on all genotypes and their genetic similarity was measured. Clustering analysis was performed independently on both types of markers. Clustering based on SSR markers separated the genotypes into three main groups originated from Korea, Thailand, and wild soybeans. On the other hand, two main groups were classified using SNP analysis. It seemed that SSR was more informative than SNP in this study. This may be due to the fact that SNP was surveyed on the smaller genomic region than SSR. Grouping based on the combined data of both markers revealed similar results to that of SNP rather than that of SSR. This might be due to the fact that more loci from SNP were considered to measure genetic relatedness than those from the SSR.

• Journal of Forest and Environmental Science
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• v.24 no.2
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• pp.61-68
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• 2008

Acrylamide is present as a contaminant in heated food products, predominantly from the precursor asparagine. Nonanchored inter simple sequence repeats (ISSRs) are arbitrary multiloci markers produced by PCR amplification with a microsatellite primer. In order to assess the feasibility of microsatellite primers as markers for DNA damage, the study was conducted on common bean (Phaseolus vulgaris L.) exposed to different concentrations of acrylamide. Polymorphisms were abundant among plant samples treated with acrylamide in comparison to control (untreated one) tested with 4- tri-nucleotide, 2 tetra-nucleotide, and 3- dinucelotide primers. The primer (CCG)4 was the best tested primer to generate polymorphism between the DNA of plants treated or not by acrylamide. Polymorphisms became evident as the presence and absence of DNA fragments in treated samples compared with the untreated one. The highest number of DNA variation on ISSR patterns was observed at the micromollar concentrations of acrylamide. Acrylamide was able to induce DNA damage in non concentration-dependent manner with effectiveness at micromollar concentrations. This study demonstrated that ISSR markers can be highly reliable for identification of DNA damage induced by acrylamide.

• Journal of Life Science
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• v.25 no.3
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• pp.257-262
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• 2015

The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (P_p) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (H_T) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (H_S) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (G_ST) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on G_ST, was very low among species of the genus Zoysia (N_m = 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.

• Korean Journal of Medicinal Crop Science
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• v.19 no.5
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• pp.347-353
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• 2011

In this study, simple sequence repeat (SSR) analyses were utilized for evaluation of genetic diversity and discrimination of 17 accessions. Five cultivars, which were developed from Korea, and 12 foreign accessions, which were collected from China, Japan, Russia and USA, were evaluated by nine markers out of 22 SSR markers. A total of 39 alleles were detected, ranging from 2 to 8, with an average of 4.3 alleles per locus. The expected heterozygosity and PIC values were 0.627 and 0.553, with a range from 0.21 (GB-PG-078) to 0.76 (GB-PG-142) and from 0.19 (GB-PG-078) to 0.70 (GB-PG-142), respectively. Four makers out of nine SSR markers, GB-PG-026, GB-PG-043, GB-PG-142 and GB-PG-177, were selected as key factors for discrimination of Korean ginseng cultivars and foreign accessions. All of Korean ginseng cultivars and foreign accessions were individually by the combination of four SSR markers. Consequently, the SSR markers developed in this study may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and foreign accessions.