• Journal of Animal Science and Technology
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• 제62권4호
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• pp.438-448
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• 2020

This study was performed to increase the accuracy of genomic estimated breeding value (GEBV) predictions for domestic pigs using single-breed and admixed reference populations (single-breed of Berkshire pigs [BS] with cross breed of Korean native pigs and Landrace pigs [CB]). The principal component analysis (PCA), linkage disequilibrium (LD), and genome-wide association study (GWAS) were performed to analyze the population structure prior to genomic prediction. Reference and test population data sets were randomly sampled 10 times each and precision accuracy was analyzed according to the size of the reference population (100, 200, 300, or 400 animals). For the BS population, prediction accuracy was higher for all economically important traits with larger reference population size. Prediction accuracy was ranged from -0.05 to 0.003, for all traits except carcass weight (CWT), when CB was used as the reference population and BS as the test. The accuracy of CB for backfat thickness (BF) and shear force (SF) using admixed population as reference increased with reference population size, while the results for CWT and muscle pH at 24 hours after slaughter (pH) were equivocal with respect to the relationship between accuracy and reference population size, although overall accuracy was similar to that using the BS as the reference.

• Bioinformatics and Biosystems
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• 제1권1호
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• pp.38-45
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• 2006

본 논문은 베이지안 네트워크를 기반으로 대규모 유전자 상호작용 네트워크를 추론하기 위한 클라이언트-서버 시스템 구조를 제시한다. 유전체 수준(genome-wide)의 대규모 유전자 상호작용 네트워크를 베이지안 네트워크 형태로 추론하기 위해서는 병렬 서버를 이용하더라도 통상 수십시간이 소요된다. 따라서, 일반적인 대화형(interactive) 독자(standalone) 시스템 구조보다는 배치형(batch) 분산(distributed) 시스템 구조가 적합하다. 본 논문에서는 그와 같은 상황에 적합한 느슨한 연결의 (loosely-coupled) 클라이언트-서버 시스템을 구현할 결과를 기술한다. 유전자 상호작용 네트워크 추론은 크게 두 단계로 나누어진다. 첫째로, 생물주석정보(biological annotation)과 유전자 발현정보(expression data)를 사용하여, 전체 유전자 집단을 서로 중복이 가능한 모듈들로 나누며, 둘째로, 각각의 모듈들에 대해 독립적인 베이지안 학습을 수행하여 추론결과를 얻고, 각 모듈들이 공통으로 포함하는 유전자를 사용하여 각 모듈의 추론결과들을 하나로 통합한다.

• Journal of Microbiology and Biotechnology
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• 제15권6호
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• pp.1240-1249
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• 2005

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

• Journal of Microbiology and Biotechnology
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• 제18권6호
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• pp.1059-1063
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• 2008

Abnormal phenotypes resulting from haploinsufficiency (HI) are due to the loss of one allele. Recent studies in budding yeast have shown that HI originates from insufficient protein levels or from a stoichiometric imbalance between subunits of protein complexes. In humans, however, HI often involves transcription factors. Therefore, the species differences in HI and the molecular mechanisms of species-specific HI remain under investigation. In this study, HI in fission yeast was systematically surveyed. HI in fission yeast affected genes related to signaling and to basic cellular processes, as observed in budding yeast. These results suggest that there are species differences in HI and that the HI that occurs in fission yeast is intermediate to HI in budding yeast and humans.

• 디지털콘텐츠학회 논문지
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• 제19권9호
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• pp.1795-1801
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• 2018

질환의 원인을 규명하기 위해 전장유전체 연관분석 (GWAS; Genome-Wide Association Study) 연구가 활발히 진행되고 유전체 레벨의 단일염기다형성 (SNP; Single-nucleotide polymorphism)이 많이 밝혀지고 있다. 그러나 단일염기다형성의 연관분석을 통해 질환이 발병하는 생물학적 메카니즘을 이해하기 어렵기 때문에 유전자, 생물학적 패스웨이 및 질환 등의 연관성 분석이 이전보다 더욱 중요하다. 본 논문에서는 단일염기다형성과 관련된 유전자와 패스웨이, 질환 정보를 검색하여 통합 분석하는 서비스를 제공하는 PRaDA 웹 시스템을 제안하였다. PRaDA는 사용자로부터 입력받은 유의한 몇몇의 단일염기다형성들과 관련된 유전자 및 패스웨이 뿐만 아니라, 유의하지 않은 다수의 단일염기다형성 집합의 간접적인 영향을 파악하기 위해 기능적으로 근접한 패스웨이를 검색하고 통계적 분석을 실행한다. 사용자들은 PRaDA가 제공하는 통합된 정보를 통해 질병의 전반적인 이해를 할 수 있다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.151-151
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• 2017

In Asia, rice production has some difficulties with reduction of farm household population and increase of elderly population. As a result, it has resulted in inefficiency and we needs to reduce labor force and improve labor productivity. Direct-seeding in rice could reduce labor and production costs, the area of direct seeding is increasing in japonica rice production in Asia. In direct seedling cultivation competition against weeds is one of most important concern. So, low temperature germinability and mesocotyl elongation should be considered. In this study, we evaluated the mesocotyl length and low temperature germination conducted association analysis using 137 korea core collections. An average length of mesocotyl among 137 core collections was skewed range from 0mm to 43mm. we searched candidate gene around target SNP. Such related traits, genome-wide association study (GWAS) analysis was carried out using GAPIT. Also, average mesocotyl length of 394 korea landrace cultivars was measured ranging from minimum 0 mm to maximum 34mm. 30 out of 394 Korea landrace cultivar conducted re-sequencing, and haplotype analysis of candidate gene. we searched these related resources, which including germination of low temperature and mesocotyl elongation. This could be used for the development of direct-seeding cultivars. The valiated accession of core collection and landrace cultivars will be used development of direct-seedling cultivar in the future.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.157-157
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• 2017

In last study, Genome-Wide Association Studies (GWAS) was conducted for cadmium content of 295 rice varieties including 137 rice core set and 157 Korea breeding varieties collected from Kongju National University. The results showed that 9 varieties had SNP allele and amino acid substitution in exon of chromosome 1. This study was aim to understanding mechanism of cadmium uptake to confirm correlation of cadmium and other mineral nutrients (Cu, Mn, Fe) among 9 rice varieties. Nine varieties were planted on polluted soil of mine in Korea and cadmium content in root, stem, leaf and it's brown rice was analyzed by ICP-MS (Inductively Coupled Plasma Mass spectrometer, Agilent 7700E, US). Results of this study showed that mechanism for cadmium uptake and accumulation was diversity among varieties. Chin-nong and Ho-nong contained higher levels of cadmium in root, but contained relatively lower levels cadmium in brown rice than other varieties. Cheong-nam, Nam-pyeong, Gan-cheok, Suan absorbed high levels of cadmium through root and then accumulated high cadmium to brown rice. Meanwhile, Yeong-deok and Su-kwang absorbed lower cadmium in root, but high cadmium was accumulated in brown rice. Correlations between cadmium and other mineral nutrients (Cu, Mn, Fe) were analyzed by using SPSS statistics 20. The contents of iron in leaf had minus correlation (p<0.05) with cooper and cadmium in root, cadmium in brown rice. Therefore understanding of cadmium uptake mechanism among varieties will be used to basic data for further breeding and phytoremediation.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.14-14
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• 2017

The discipline of plant breeding is experiencing a renaissance impacting crop improvement as a result of new technologies, however fundamental questions remain for predicting the phenotype and how the environment and genetics shape it. Inexpensive DNA sequencing, genotyping, new statistical methods, high throughput phenotyping and gene-editing are revolutionizing breeding methods and strategies for improving both quantitative and qualitative traits. Genomic selection (GS) models use genome-wide markers to predict performance for both phenotyped and non-phenotyped individuals. Aerial and ground imaging systems generate data on correlated traits such as canopy temperature and normalized difference vegetative index that can be combined with genotypes in multivariate models to further increase prediction accuracy and reduce the cost of advanced trials with limited replication in time and space. Design of a GS training population is crucial to the accuracy of prediction models and can be affected by many factors including population structure and composition. Prediction models can incorporate performance over multiple environments and assess GxE effects to identify a highly predictive subset of environments. We have developed a methodology for analyzing unbalanced datasets using genome-wide marker effects to group environments and identify outlier environments. Environmental covariates can be identified using a crop model and used in a GS model to predict GxE in unobserved environments and to predict performance in climate change scenarios. These new tools and knowledge challenge the plant breeder to ask the right questions and choose the tools that are appropriate for their crop and target traits. Contemporary plant breeding requires teams of people with expertise in genetics, phenotyping and statistics to improve efficiency and increase prediction accuracy in terms of genotypes, experimental design and environment sampling.

• Asian-Australasian Journal of Animal Sciences
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• 제16권8호
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• pp.1087-1092
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• 2003

As an experimental reference population, crosses between Korean native pig and Landraces were established and information on growth traits was recorded. Animals were genotyped for 24 microsatellite markers covering chromosomes 2, 6, and 7 for partial-genome scan to identify chromosomal regions that have effects on growth traits. quantitative trait loci (QTL) effects were estimated using interval mapping by the regression method under the line cross models with a test for imprinting effects. For test of presence of QTL, chromosome-wide and single position significance thresholds were estimated by permutation test and normal significance threshold for the imprinting test were derived. For tests against the Mendelian model, additive and dominance coefficients were permuted within individuals. Thresholds (5% chromosome-wide) against the no-QTL model for the analyzed traits ranged from 4.57 to 4.99 for the Mendelian model and from 4.14 to 4.67 for the imprinting model, respectively. Partial-genome scan revealed significant evidence for 4 QTL affecting growth traits, and 2 out of the 4 QTLs were imprinted. This study demonstrated that testing for imprinting should become a standard procedure to unravel the genetic control of multi-factorial traits. The models and tests developed in this study allowed the detection and evaluation of imprinted QTL.

• Asian-Australasian Journal of Animal Sciences
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• 제27권10호
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• pp.1381-1386
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• 2014

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from $0.42{\pm}0.14$ in zebu to $0.148{\pm}0.14$ in gayal with significant heterozygosity deficiency of 0.06 ($F_{IS}$) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation ($F_{ST}=0.33$) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.