• Horticulture, Environment, and Biotechnology : HEB
• /
• v.59 no.6
• /
• pp.889-897
• /
• 2018

Currently, there is a lack of genetic markers capable of effectively detecting polymorphisms in Clematis. Therefore, we developed new markers to investigate inter- and intraspecific diversity in Clematis. Based on the complete chloroplast genome of Clematis terniflora, simple sequence repeats were explored and primer pairs were designed for all ten adequate repeat regions (cpSSRs), which were tested in 43 individuals of 11 Clematis species. In addition, the nuclear ITS region was sequenced in 11 Clematis species. Seven cpSSR loci were found to be polymorphic in the genus and serve as markers that can distinguish different species and be used in different genetic analyses, including cultivar identification to assist the breeding of new ornamental cultivars.

• Mycobiology
• /
• v.45 no.2
• /
• pp.105-109
• /
• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.9
• /
• pp.1189-1195
• /
• 2014

A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

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

• Journal of Plant Biotechnology
• /
• v.43 no.2
• /
• pp.181-188
• /
• 2016

In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata. We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

• Fisheries and Aquatic Sciences
• /
• v.26 no.12
• /
• pp.752-761
• /
• 2023

Genetic diversity serves as the basis for selecting and genetically enhancing any culturable species in aquaculture. Here, two different strains of wild (River Ravi and River Kabul) and six captive-bred strains of Labeo rohita from various provinces were se- lected, and genetic diversity among them was evaluated using three different microsatellite markers, i.e., Lr-28, Lr-29, and Lr-37, and one mitochondrial CO1 (Cytochrome c oxidase subunit 1) gene. Different strains of L. rohita were collected, and part of their caudal fin was cut and preserved in ethanol for DNA extraction and determination of genetic diversity among them. Results in- dicated that selected markers were polymorphic with polymorphic information content (PIC) content values above 0.5 with the highest in Lr-28 followed by Lr-29 and then Lr-37. The observed heterozygosity (Ho) of all strains was higher (Avg: 0.731) but less than the expected heterozygosity (He). Moreover, TMs and WRs showed the highest He, while TKs showed the lowest, He. Over- all, inbreeding coefficient (FIS) values observed for all strains with selected markers were positive. The DNA barcoding with the CO1 gene revealed genetic variation among various strains, as demonstrated by the clades in the phylogenetic tree separating the strains into two distinct clusters that then divided into sub-clusters. In conclusion, TMs showed the highest heterozygosity as compared to other strains. Overall results provide the baseline data for the initiation of the genetic improvement program.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.49 no.4
• /
• pp.358-362
• /
• 2004

In order to develop molecular markers related to stay green phenotype, AFLP analysis was conducted using near-isogenic lines for either stay green or non stay green trait. Both lines have characteristics of multi-ear and tillers (MET). Two out of 64 primer combinations of selective amplification identified three reproducible polymorphic fragments in MET corn with stay green. Both of E+AGC/M+CAC and E+AAG/M+CAA primer combinations produced two and one specific polymorphic fragments linked to stay green trait, respectively. For the conversion of AFLPs to sequence tag sites (STSs), primers were designed form both end sequences of each two polymorphic fragments. One fragment, which was amplified with E+AAG/M+CAA primer combinations, possessed 298 bp long and showed a $91\%$ homology with maize retrotransposon Cinful-l. One out of two polymorphic fragments produced with E+AGC/M+CAC primer combination had 236 bp long and matched a $96\%$ homology with an intron region of 22kDa alpha zein gene cluster in Zea mays. One out of two PCR fragments amplified with MET2 primer set in the stay green MET was not produced in the non-stay green MET. The developed AFLP and STS marker could be used as an efficient tool for selection of the stay green trait in the MET inbred.

• Radiation Oncology Journal
• /
• v.11 no.1
• /
• pp.83-90
• /
• 1993

During the period from January, 1975, to June, 1989, one hundred patients with histopathologically proven polymorphic reticulosis in the upper respiratory tract were treated with radiation therapy and the analysis of treatmemt results was undertaken. One hundred patients (69 males, 31 females) with a mean age of 46 years (range 12-79 years) were presented. Nasal cavity was the most frequent site of involvement ($56{\%}$), and 44 cases had multifocal sites of involvement. The incidence of cervical lymph node metastasis at initial diagnosis was $24{\%}$. Staging was determined by Ann-Arbor classification, retrospectively. The number of patients of stage IE, IIE, IIIE and IVE were 35, 60, 1, and 4, respectively. The overall 5 year actuarial survival rates were $38.4{\%}$. The difference in 5 year survival rates between patients with stage IE and IIE, with solitary and multiple, with CR and PR after irradiation were significant statistically. For the analysis of failure patterns, failure sites include the following: local failure alone (30/55=$54.6{\%}$), systemic failure alone (9/55=$16.4{\%}$), both local and systemic failure (16/55=$29.0{\%}$). Retrograde slide review was available in 29 cases of PMR with respect to histopathologic bases, and immunohistochemical studies were performed using MT1 and DACO-UCHL-1 as T-cell markers, MB2 as a B-cell marker and alpha-1-antichymotrypsin as a histiocytic markers. All that 29 cases showed characteristic histologic features similar to those of peripheral T-cell lymphoma and showed positive reactio to the T-cell marker. These findings suggest strongly that quite a significant portion of PMR may be in fact T-cell lymphoma.

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

• Journal of Life Science
• /
• v.24 no.7
• /
• pp.707-712
• /
• 2014

We evaluated the phenetic relationships within six taxa of genus Oxalis L. in Korea with random amplified polymorphic DNA (RAPD) markers. Ten primers produced 125 bands for six taxa, and the mean number of bands per primer was 12.5. Across the six taxa, 121 (96.8%) bands were polymorphic, and only four were monomorphic. The mean number of RAPD phenotypes across the six taxa varied from 3.6 (O. stricta and O. corymbosa) to 4.8 (O. corniculata for. rubrifolia). In a simple measure of intraspecies variability according to the percentage of polymorphic bands, O. stricta and O. corymbosa exhibited the lowest variation (28.8%), and O. corniculata for. rubrifolia showed the highest (38.4%). A mean of 32.7% of the loci was polymorphic within taxa. The total interspecies genetic diversity ($H_T$) and intraspecies genetic diversity ($H_S$) was 0.362 and 0.122, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among species ($G_{ST}$) was 0.663. This indicates that about 66.3% of the total variation was among species. The node of O. stricta and O. corniculata for. rubrifolia was strongly supported, with a high bootstrap value in the NJ tree and sistered with O. corniculata. According to RAPD analysis, the number of chromosomes was not congruent with a phenetic relationship.