• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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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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• 제38권3호
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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.

• 생명과학회지
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• 제29권1호
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• pp.1-8
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• 2019

한우(한국 재래 소)에서 반수체형 페이징을 위한 고밀도 시퀀싱을 이용한 비교 분석 논문은 많지가 않다. 이런 고밀도 시퀀싱 플랫폼 중에서, 일루미나에서 서비스 하는 Truseq Synthetic Long-Read Haplotyping 시퀀싱 플랫폼(TSLRH)과 10X Genomics에서 서비스하는 The Chromium Genome 시퀀싱 플랫폼을 특별히 비교 분석하는 논문은 없다. 우리는 한우 연구소의 한우 종모우(아이디: TN1505D2184 or 27214)의 정액에서 DNA를 추출하였으며, 이 DNA로부터 각각의 시퀀싱 플랫폼을 이용하여 시퀀싱 데이터를 생산하였다. 그 후, 우리는 각각의 시퀀싱 플랫폼에 맞는 분석 방법을 이용하여 단일염기서열변이들은 찾아냈다. 그 결과, TSLRH과 10XG의 전체 리드 수는 각각 355,208,304, 1,632,772,004, 맵핑 리드의 개수는 351,992,768(99.09%), 1,526,641,824(93.50%), Q30(%)은 89.04%, 88.60%, 평균 밀도는 13.04X, 74.3X, 가장 긴 페이즈 블락은 1,982,706bp, 1,480,081 bp, N50 페이즈 블락은 57,637 bp, 114,394 bp, 전체 단일염기서열변이는 4,534,989, 8,496,813, 전체 페이징 비율은 72.29%, 87.67%였다. 더욱이, 우리는 각각의 시퀀싱 플랫폼을 비교해서 각각의 시퀀싱 플랫폼의 고유한 단일염기서열변이와 두 시퀀싱 플랫폼에서 공통적으로 존재하는 단일염기서열변이를 각 염색체 별로 확인하였으며, 단일염기서열변이의 개수는 염색체 길이에 정비례한다는 결과를 확인하였다. 결론적으로, 본 연구에서 추천하는 바는 연구비가 충분하지 않을 시에는 TSLRH 보다 10XG을 사용하는 것을 추천한다. 왜냐하면 전체 리드 및 단일염기서열변이 개수, N50 페이즈 블락, 가장 긴 페이즈 블락, 페이즈 비율 그리고 평균 밀도 등이 TSLRH 보다 10XG가 더 높거나 좋기 때문이다.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2002년도 추계 학술발표회 논문집
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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.

• 한국산림과학회지
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• 제94권3호통권160호
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• pp.178-182
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• 2005

소나무의 2년생 인공교배(人工交配) 전형매차대목(全兄妹次代木) 114개체를 대상으로 화분친(花粉親)이 아닌 개체의 화분에 의해 생성된 차대목(次代木)을 식별하기 위하여 부계유전(父系遺傳)되는 반수체(半數體) 표지자인 cpSSR 표지자 분석을 실시하였다. 3개의 cpSSR primer를 이용한 PCR 분석을 통하여 화분친(花粉親)과 3개 모수(母樹)의 haplotype 조합을 결정하고, 이에 의해 각 개체의 DNA 지문이 확인되었다. 동일한 cpSSR primer를 사용하여 전형매차대(全兄妹次代) 114개 개체목의 haplotype을 확인하고 이를 화분친(花粉親) 및 3개 모수(母樹)에서 확인된 haplotype 조합과 비교한 결과, 이들 중 14개체에서 인공교배(人工交配) 화분친(花粉親)과 다른 cpDNA haplotype이 확인되어 이들이 교배에 사용된 화분친(花粉親)이 아닌 타개체로부터 유입된 화분에 의해서 생성된 개체로 동정되었다. 특히, 강원30으로부터 생산된 차대(次代) 중 한 개체목은 불완전한 제웅(除雄)이나 인공교배(人工交配)시 모수(母樹)에서 생산된 화분의 유입으로 인해서 야기된 자가교배(自家交配)에 의해서 생성되었을 가능성이 매우 높은 것으로 나타났다. 본 연구에서 분석된 cpSSR 지문분석은 향후 자연림내 친계차대목(親系次代木) 감별과 삽목, 접목 및 조직배양에 의한 무성번식묘(無性繁殖苗)의 동정, 순수(純粹) 전형매차대(全兄妹次代)의 확인 등 식물법의학적(植物法醫學的) 분석법(分析法)에 유용하게 활용될 수 있을 것으로 기대된다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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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.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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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.

• 동의생리병리학회지
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• 제16권6호
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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.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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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.

• 정보처리학회논문지B
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• 제16B권2호
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• pp.157-161
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• 2009

일배체형 조합 문제를 해결하기 위해 제시된 MLF(Minimum Letter Flips) 모델이나 WMLF(Weighted Minimum Letter Flips) 모델은 유전자형 정보를 도입함으로써 오류와 손실이 많을 때에도 높은 정확도를 얻을 수 있다. 그리고 MLF 모델에 비해 가중치 버전인 WMLF모델의 정확도가 높다는 사실도 밝혀졌다. 본 논문에서는 유전자형 정보상의 동형(homozygous)의 분포 비율과 유전자 서열판독기계의 성능에 따른 신뢰도의 차이를 매개변수로 하여 두 모델을 구체적으로 비교, 분석한다. 두 모델의 성능 비교를 위해 신경망과 유전자 알고리즘을 사용한다. 실험결과 동형의 비율이 크고 판독기계의 성능이 좋으면 특히 손실율과 오류율이 높은 경우에 WMLF/GI 모델의 정확도가 더 우수함을 보인다.