• Korean Journal of Microbiology
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• v.36 no.4
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• pp.249-253
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• 2000

The genetic diversity among Korean cyanobacteria was assessed by restriction fragment length polymorphism(RFLP) analysis of PCR products from the phycocyanin locus. Strains of all the genera tested were successfully amplified, and the size of amplified fragments was approximately 700bp. The restriction patterns generated by AluI, MspI, and HaeIII were conserved for strains within each of genera studied and were specific to the genus level. Intrageneric delineation of strains was revealed by the enzyme, CfoI for members of genera Anabeana and Synechocystis. Phenogram derived from the different RFLP patterns revealed a coherent cluster among Anabeana, Chlorogloea, and Synechocystis strains. PC-RFLP methods provided useful tools for classification of cyanobacteria.

• Molecules and Cells
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• v.37 no.1
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• pp.36-42
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• 2014

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

• Genomics & Informatics
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• v.20 no.2
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• pp.17.1-17.11
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• 2022

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

• Korean Journal of Plant Taxonomy
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• v.37 no.2
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• pp.131-141
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• 2007

Genetic variation of Ilex cornuta Lindley et Paxton was examined by sequence analyses of ITS for 65 individuals from Korea and China. The length of ITS 1 ranged from 253 to 259 bp. The 5.8S was 159 bp and ITS2 was observed to be 231 bp. A total of 8 different ITS types (Single Nucleotide Polymorphism haplotypes), which showed the difference of 1 - 6 bp, were detected from 65 individuals. The sequence polymorphisms of ITS appeared at 9 different sites. All of four individuals collected at Daejeong-eup in Jeju-do exhibited different types, but all individuals from Naju-si and Muan-gun in Jeollanam-do were identical. The variation of ITS was higher in Jeju-do population than in inland population. Since I. cornuta contains various types of ITS sequences, ITS analyses will provide important information on genetic diversity and conservation of this species.

• Horticultural Science & Technology
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• v.31 no.6
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• pp.798-806
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• 2013

Precise, fast, and cost-effective identification of crop cultivars is essential for plant breeder's rights. Traditional methods for identification of persimmon cultivars are based on the evaluation of sets of morphological characteristics. However, it is difficult to distinguish closely related cultivars using only morphological traits. This study was conducted to develop DNA markers for identification of the 32 persimmon cultivars in Korea and Japan. A total of 309 randomly amplified polymorphic DNA (RAPD) markers were identified using 40 different random primers. Various number of polymorphic bands ranged from 4 (OPP-08) to 14 (UBC159) were detected with an average of 7.7. Resulting 57 RAPD fragments were selected, and their sequences were determined for developing sequence characterized amplified region (SCAR) markers. As a result, 15 of 57 RAPD fragments were successfully converted to SCAR markers. Single polymorphic bands of the same size as or smaller than the RAPD fragments were amplified depending on SCAR markers. Among these markers, a combination of eight SCAR markers (PS225_200, PSN05_420, PSF13_523, PSN11_540, PS372_567, PS485_569, PSP08_635, and PS631_735) provided sufficient polymorphisms to identify 32 persimmon cultivars. These newly developed markers will be a fast and reliable tool to identify persimmon cultivars.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• Journal of Life Science
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• v.16 no.6
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• pp.1001-1005
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• 2006

The objective of this study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for genetic diversity assessment and identification of rice varieties. The 23 primers selected from 50 SSR primers showed polymorphisms in the 21 rice varieties. The 2 to 9 SSR alleles were detected for each locus with an average of 3.00 alleles per locus. The polymorphism information content (PIC) ranged form 0.091 to 0.839. Based on band patterns, UPGMA cluster analysis was conducted. These varieties were separate into 4 groups corresponding to rice ecotype and pedigree information and genetic distance of cluster ranging from 0.59 to 0.92. The 4 SSR primer sets (RM206, RM225, RM418, RM478) selected form 23 polymorphic primers were differentiated all the rice variety from each other by markers genotypes. These markers may be used wide range of practical application in variety identification of rice.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.722-729
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• 2015

Powdery mildew (PM) caused by Podosphaera aphanis is a major disease that can result in significant yield losses in strawberry (Fragaria ${\times}$ ananassa Duchesne). For preventing PM, pesticides are usually applied in strawberry. In this study, molecular markers were developed to increase breeding efficiency of PM-resistance cultivars by marker-assisted selection (MAS). An $F_2$ population derived from a cross between PM-resistance 'Seolhyang' and PM-susceptibility 'Akihime' was evaluated for disease resistance to PM and RAPD (random amplification of polymorphic DNA)-BSA (bulked segregant analysis). Among 200 RAPD primers tested, OPE10 primer amplified a 311bp-band present in with 331bp. Sequence alignment performed for searching polymorphisms and six single nucleotide polymorphism (SNP) were found in amplified regions. To develop polymorphic marker for distinguishing between resistant and susceptible, RAPD was converted to cleaved amplified polymorphic sequence (CAPS) marker. Among restriction enzymes associated with six SNPs, Eae I (Y/GGCCR) was successfully digested to 231bp in susceptible. The results suggest that the selected CAPS marker could be used for increasing efficiency of selecting powdery mildew resistant strawberry in breeding system.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8319-8324
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• 2014

Although genetic markers identifying women at an increased risk of developing breast cancer exist, the majority of inherited risk factors remain elusive. Mutations in the BRCA1/BRCA2 gene confer a substantial increase in breast cancer risk, yet routine clinical genetic screening is limited to the coding regions and intronexon boundaries, precluding the identification of mutations in noncoding and untranslated regions. Because 3' untranslated region (3'UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we aimed to determine genetic variation in the 3'UTR of BRCA1/BRCA2 in familial and early-onset breast cancer patients with and without mutations in the coding regions of BRCA1/BRCA2 and to identify specific 3'UTR variants that may be risk factors for cancer development. The 3'UTRs of the BRCA1 and BRCA2 genes were screened by heteroduplex analysis and DNA sequencing in 100 patients from 46 BRCA1/2 families, 54 non-BRCA1/2 families, and 47 geographically matched controls. Two polymorphisms were identified. SNPs $c.^*1287C$ >T (rs12516) (BRCA1) and $c.^*105A$ >C (rs15869) (BRCA2) were identified in 27% and 24% of patients, respectively. These 2 variants were also identified in controls with no family history of cancer (23.4% and 23.4%, respectively). In comparison to variations in the 3'UTR region of the BRCA1/2 genes and the BRCA1/2 mutational status in patients, there was a statistically significant relationship between the BRCA1 gene polymorphism $c.^*1287C$ >T (rs12516) and BRCA1 mutations (p=0.035) by Fisher's Exact Test. SNP $c.^*1287C$ >T (rs12516) of the BRCA1 gene may have potential use as a genetic marker of an increased risk of developing breast cancer and likely represents a non-coding sequence variation in BRCA1 that impacts BRCA1 function and leads to increased early-onset and/or familial breast cancer risk in the Turkish population.