• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.215-215
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• 2022

Starch synthase proteins (SSI, SSII and SSIII) in rice are mainly involved in amylopectin synthesis mediating its chain elongation, and the functional loss of SSII can increase amylose accumulation through decreasing of amylopectin chain proportions. For purposes of identifying functional haplotypes and evolutionary analyses of this gene, SSII-1, we investigated 374 rice accessions belonging to different subgroups of origins. We subsequently performed bioinformatic analyses on their variations through haplotyping, resequencing and structuring based on different classified populations. Haplotyping of cultivated rice accessions using genetic variations within SSII-1 genomic region of chromosome 10 revealed a total of 8 haplotypes, representing 6 functional haplotypes by 4 non-synonymous SNPs of three different exons (1, 4 and 10), which effect on protein structure. Higher nucleotide diversity value was found in wild group (0.0055) compared to any of cultivated subpopulations, of which aus showed the most reduction of diversity value (0.0003). Tajima's D analysis exhibits the most Tajima's D value only in admixture group (0.3600) which appears to be the cause of a sudden population contraction by rare alleles scarcity. A clear separation of some wild accessions from the admixed cultivated subpopulations was observed in PCA and phylogenetic analysis. Similar admixed pattern of population structure was estimated with an increased K values of 2 to 8 where genetic components of almost all cultivated subpopulations were shared with the wild which can also be subsequently estimated by very low F_ST-values by -0.011 (wild-aromatic) and -0.003 (wild-admixture).

• Clinical and Experimental Reproductive Medicine
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• v.38 no.3
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• pp.126-134
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• 2011

Preimplantation genetic diagnosis (PGD) is gradually widely used in prevention of gene diseases and chromosomal abnormalities. Much improvement has been achieved in biopsy technique and molecular diagnosis. Blastocyst biopsy can increase diagnostic accuracy and reduce allele dropout. It is cost-effective and currently plays an important role. Whole genome amplification permits subsequent individual detection of multiple gene loci and screening all 23 pairs of chromosomes. For PGD of chromosomal translocation, fluorescence $in-situ$ hybridization (FISH) is traditionally used, but with technical difficulty. Array comparative genomic hybridization (CGH) can detect translocation and 23 pairs of chromosomes that may replace FISH. Single nucleotide polymorphisms array with haplotyping can further distinguish between normal chromosomes and balanced translocation. PGD may shorten time to conceive and reduce miscarriage for patients with chromosomal translocation. PGD has a potential value for mitochondrial diseases. Preimplantation genetic haplotyping has been applied for unknown mutation sites of single gene disease. Preimplantation genetic screening (PGS) using limited FISH probes in the cleavage-stage embryo did not increase live birth rates for patients with advanced maternal age, unexplained recurrent abortions, and repeated implantation failure. Polar body and blastocyst biopsy may circumvent the problem of mosaicism. PGS using blastocyst biopsy and array CGH is encouraging and merit further studies. Cryopreservation of biopsied blastocysts instead of fresh transfer permits sufficient time for transportation and genetic analysis. Cryopreservation of embryos may avoid ovarian hyperstimulation syndrome and possible suboptimal endometrium.

• Journal of Life Science
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• v.29 no.1
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• pp.1-8
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• 2019

In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using highdepth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.

• Proceedings of the Korean Statistical Society Conference
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• 2002.11a
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• pp.203-207
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• 2002

Post-genome 시대를 맞이하여 인류는 전 유전체에서의 염기서열에 대한 정보를 가질 수 있게 되었다. 이러한 정보를 이용하여서 인간에게 나타나는 다양성을 설명하기 위해서 SNP(Single Nucleotide Polymorphism)의 연구가 활발히 되고 있다. 하지만 인간 체세포의 염색체는 2쌍으로 되어있기 때문에 이러한 정보가 어떠한 쌍의 조합(haplotype)으로 나타나는가를 고려하여야한다. 현재 실험적 방법으로 이를 고려하기에는 여러 가지 제약이 따르므로 통계적인 방법으로 이를 모형화하려는 노력(in silico haplotyping)이 시도되고 있다. 이 논문에서는 통계적으로 haplotype을 정하는 대표적인 알고리즘인 Clark's algorithm, E-M algorithm 등에 대한 고찰을 통하여 유전체통계학에 대한 소개를 하고자 한다.

• Journal of Korean Society of Forest Science
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• v.94 no.3 s.160
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• pp.178-182
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• 2005

To identify the seedlings from controlled pollination between one paternal tree and three maternal trees of Japanese red pine, cpSSR markers of the paternally inherited haploid genome were analyzed in two year old 114 seedlings of full sib families. Individual specific DNA fingerprint like haplotypes of the parental trees were determined by PCR with three cpSSR primers. Haplotypes of the 114 seedlings were also identified by PCR with the same primers. On the basis of the comparison of cpDNA haplotypes of the 114 seedlings with those of the parental trees, 14 seedlings revealed to have distinguished haplotypes from those of the paternal tree. It was tentatively concluded that they were generated via pollination with the non-paternal trees. A seedling of Gangwon30 revealing non-paternal haplotype might have been generated via self pollination with the pollens of maternal tree through improper emasculation or contamination during artificial pollination. DNA fingerprint like cpSSR profiles observed in this study could be successfully applied to the various plant forensic analyses, such as identification of siblings of individual trees, asexually reproduced ramets of a specific clone, vegetatively propagated individuals via tissue culture, and pure full sib progenies.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.221-228
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• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.218-218
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• 2022

Granules-bound starch synthase II (GBSSII), one of the isoforms of granule-bound starch synthase (GBSS), is responsible for amylose synthesis by expressing in non-storage tissues such as leaf, stem, root, and pericarp. Up to date, little is known about this gene functions and basic knowledge of heritable characteristics of this gene, GBSSII. We identified functional haplotypes and performed evolutionary analyses on the GBSSII using 374 rice accessions (320 Korean bred and 54 wild) based on the classified groups. A total of 14 haplotypes were found, and almost all haplotypes (13) were functional, carrying 19 non-synonymous SNPs in two exons (exons 1 and 2). The lowest nucleotide diversity was detected in Tropical japonica (0.00145), while the highest pi-value was in Aus (0.01081), illustrating the signal of this gene evolution. The highest Tajima's D value in Aus (1.6380) indicates GBSSII gene domestication signature under balancing selection, while the lowest Tajima's D value in Temperate japonica (-0.8243) highlights that they were under positive selection, which may be purified due to the excess of rare alleles. The highest genetic differentiation was observed between Tropical japonica and aroma (F_ST = 0.921928). In contrast, the highest interbreed level was detected in Aus-admixture (F_ST = -0.20157). The genetic relatedness between and or among the wild and cultivated subpopulations was revealed through PCA, population structure, and phylogenetic analyses.

• Journal of Physiology & Pathology in Korean Medicine
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• v.16 no.6
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• pp.1201-1206
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• 2002

In oriental medicine, human being is classified into four groups according to their body constitution status (;tae-yang, tae-eum, so-yang, and so-eum persons) considering the differences in function of internal organs and characteristics. Four body constitution, called 'sa-sang' has been recognized as an important factor for diagnosing the patients before madical teratment. Yet, the criteria to divide body constitutions or its scientific principle are not clearly defined. As an initial effort to elucidate biological priciples underlying four body constitution groups, we studied genetic variations among three constitution groups (tae-eum, so-yang, and so-eum persons). Noting distinct responses to ingested food and administered drugs among three groups, SNPs and haplotype experiments were performed in 2D6, 2C9, and 1A2 DNA regions of the cytochrome P450 gene. Significant variability in SNPs types was found in 2D6 region. Moreover, haplotyping in 2D6 region showed relatively high occurrences of haplotype 3 and 5 in so-eum person, haplotype 6 in tae-eum person, and hyplotype 1 in so-yang person. These results indicate that individuals with different body constitutions respond differently to ingested food and drugs, which might reflect constitution-specific genetic background. The genetic approach would therefore be useful to reveal intrinsic differences among four constitution body groups in the responsiveness to various drugs and external stimulations to human body.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.158-158
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• 2017

The purpose of this study was to identify the candidate genes involved in selenium content in brown rice. Rice (Oryza sativa L.) was important crop including diverse functional substance such as carbohydrate, protein, lysine and tocopherol, mineral. Especially, selenium as nutritionally important minerals, it was known to activate the immune system, antioxidant effect and inhibition of carcinogenesis. Also recommended daily requirements of the United States and the United Kingdom were 55 to 90 ug for selenium. Therefore, selenium content in brown rice of core-set were analyzed by using ICP-MS (Inductively Coupled Plasma Mass Spectrometer) and GWAS (Genome Wide Association Study) was conducted to search for candidate genes in this study. The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

• The KIPS Transactions:PartB
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• v.16B no.2
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• pp.157-161
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• 2009

Minimum Letter Flips(MLF) and Weighted Minimum Letter Flips(WMLF) can perform the haplotype reconstruction more accurately from SNP fragments when they have many errors and gaps by introducing the related genotype information. And it is known that WMLF is more accurate in haplotype reconstruction than those based on the MLF. In the paper, we analyze two models under the conditions that the different rates of homozygous site in the genotype information and the different confidence levels according to the sequencing quality. We compare the performance of the two models using neural network and genetic algorithm. If the rate of homozygous site is high and sequencing quality is good, the results of experiments indicate that WMLF/GI has higher accuracy of haplotype reconstruction than that of the MCIH especially when the error rate and gap rate of SNP fragments are high.