• 자연과학논문집
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• 제11권1호
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• pp.45-54
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• 1999

4-NQO에 대한 감수성을 이용한 A.nidulans uvs 유전자들의 epistatic grouping은 자외선 및 MMS의 감수성을 이용한 grouping과 동일한 결과를 보였다. 한편, MMS에 대한 감수성을 기준으로 분류한 epistasis group에서 uvsA는 UvsF group 유전자인 uvsF 및 uvsH와 synergistic interaction을 보였으며, uvsA;uvsB 및 uvsA;uvsC 이배체는 uvsB, uvsC의 반수체와 동일한 감수성을 나타내었다. Germination한 뒤 4시간 후의 자외선 감수성을 기준으로 한 uvsI의 epistatic grouping은 conidia 상태에서 자외선을 쬐어 조사한 grouping과 유사하여, uvsH, uvsC, uvsB와 synergistic interaction을 보였다. 하지만, quiescent conidia 상태에서의 additive effect를 보인 uvsI와 uvsF 돌연변이체는 4h germination 후에는 epistatic interaction을 나타내었다. uvsI 돌연변이체의 Intergenic-intragenic recombination frequency는 야생주와 유사하였다.

• 한국가금학회지
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• 제48권2호
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• pp.51-58
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• 2021

지방산 조성은 고기의 풍미에 영향력 있는 중요한 경제 형질 중 하나이며, 다양한 유전자들의 효과가 알려져 있다. 본 연구는 한국 재래닭의 지방산 조성에 유의적인 영향을 미치는 것으로 조사된 6개의 후보 유전자들(DEGS1, ELOVL6, FABP3, FABP4, FASN, SCD)의 51개 SNP 조합에 대한 추가적인 분석결과로, 선행연구를 통하여 확인된 SNP 조합들이 가지는 상위성 효과에 대하여 조사하였다. 본 연구를 통하여 매우 다양한 유형의 SNP 조합들이 한국 재래닭의 지방산 조성에 영향을 미치는 것으로 확인되었으며, 추후에 지방산 조성과 같은 다유전자성 형질들을 실제 육종 프로그램에 활용하기 위해서는 이러한 분석이 이루어져야 될 것으로 생각된다. 본 연구 결과는 한국 재래닭의 육질, 특히 지방산 조성의 개선을 위한 유전학적인 정보를 제공할 수 있을 것으로 생각된다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.267-267
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• 2022

Glutinous rice is a key grain quality trait occupying an important part during rice processing in most rice growing areas. Amylose content (AC) of rice determine eating quality which is one of the major traits in rice breeding program. In this study, a gene pyramiding approach was used to introduce two dull genes, responsible for low amylose contents, for glutinous rice breeding using marker assisted selection (MAS). Two dull genes were located on chromosome 6 (wx-mq, AC: 12.7 %) and chromosome 10 (du1, AC: 10.3%), respectively. To test whether these two dull genes have an epistatic interaction, we developed an F₂ population by crossing two nearly isogenic lines(NILs) harboring wx-mq and du1. Gene based marker and KASP marker were used to select NILs(NIL-nor, NIL-wxmq, NIL-du1, and NIL-wxmq/du1) from the F2 population. A two-way ANOVA revealed an epistatic interaction between the two genes in the F2 population. The mean of Amylose contents for NIL-nor, NIL-wxwq, NIL-(du1, and NIL-wxmq/du1 were 17.3%, 12.5%, 9.7%, and 7.2%, respectively. This interaction was confirmed by an analysis of NILs indicating that both genes are involved in the same genetic mechanism controlling amylose contents. This result will be useful for rice breeding related to amylose content.

• Animal Bioscience
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• 제37권4호
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• pp.622-630
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• 2024

Objective: Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP). Methods: Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip. Results: The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits. Conclusion: This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

• Journal of Plant Biotechnology
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• 제44권4호
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• pp.349-355
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• 2017

The amino acid composition of rice is a major concern of rice breeders because amino acids are among the most important nutrient components in rice. In this study, a genetic map was constructed with a population of 134 recombinant inbred lines (RILs) from a cross between Dasanbyeo (Tongil-type indica) and TR22183 (temperate japonica), as a means to detect the main and epistatic effect quantitative trait loci (QTLs) for the amino acid content (AAC). Using a linkage map which covered a total of 1458 cM based on 239 molecular marker loci, a total of six main-effect QTLs (M-QTLs) was identified for the content of six amino acids that were mapped onto chromosome 3. For all the M-QTLs, the TR22183 allele increased the trait values. The QTL cluster (flanked by id3015453 and id3016090) on chromosome 3 was associated with the content of five amino acids. The phenotypic variation, explained by the individual QTLs located in this cluster, ranged from 10.2 to 12.4%. In addition, 26 epistatic QTLs (Ep-QTLs) were detected and the 25 loci involved in this interaction were distributed on all nine chromosomes. Both the M-QTLs and Ep-QTLs detected in this study will be useful in breeding programs which target the development of rice with improved amino acid composition.

• Journal of Microbiology
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• 제39권2호
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• pp.102-108
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• 2001

DNA damage response has a central role in the maintenance of genomic integrity while mutations in related genes may result in a range of disorders including neoplasic formations. The uvsZl characterized in this report is a navel uvs mutation in Aspergillus nidulans, resulting in a nucleotide excision repair (NER) phenotype: UV-sensitivity before DNA synthesis (quiescent cells), high UV-induced mutation frequency and probable absence of involvement with mitotic and meiotic recombinations. The mutation is recessive and nan-allelic to the previously characterized uvsA101 mutation, also located on the paba-y interval on chromosome I. uvsZl skewed wild-type sensitivity to MMS, which suggests non-involvement of this mutation with BER. Epitasis tests showed that the uvsZ gene product is probably involved in the same repair pathways as UVSB or UVSH proteins. Although mutations in these proteins result in an NER phenotype, UVSB is related with cell cycle control and UVSH is associated with the post-replicational repair pathway. The epistatic interaction among uvsZl and uvsB413 and uvsH77 mutations indicates that different repair systems may be related with the common steps of DNA damage response in Aspergillus nidulans.

• Genomics & Informatics
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• 제12권4호
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• pp.216-224
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• 2014

Gastritis is a common but a serious disease with a potential risk of developing carcinoma. Helicobacter pylori infection is reported as the most common cause of gastritis, but other genetic and genomic factors exist, especially single-nucleotide polymorphisms (SNPs). Association studies between SNPs and gastritis disease are important, but results on epistatic interactions from multiple SNPs are rarely found in previous genome-wide association (GWA) studies. In this study, we performed computational GWA case-control studies for gastritis in Korea Associated Resource (KARE) data. By transforming the resulting SNP epistasis network into a gene-gene epistasis network, we also identified potential gene-gene interaction factors that affect the susceptibility to gastritis.

• Communications for Statistical Applications and Methods
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• 제29권1호
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• pp.65-83
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• 2022

Although various statistical methods have been developed to map time-dependent genetic factors, most identified genetic variants can explain only a small portion of the estimated genetic variation in longitudinal traits. Gene-gene and gene-time/environment interactions are known to be important putative sources of the missing heritability. However, mapping epistatic gene-gene interactions is extremely difficult due to the very large parameter spaces for models containing such interactions. In this paper, we develop a Gaussian process (GP) based nonparametric Bayesian variable selection method for longitudinal data. It maps multiple genetic markers without restricting to pairwise interactions. Rather than modeling each main and interaction term explicitly, the GP model measures the importance of each marker, regardless of whether it is mostly due to a main effect or some interaction effect(s), via an unspecified function. To improve the flexibility of the GP model, we propose a novel grid-based method for the within-subject dependence structure. The proposed method can accurately approximate complex covariance structures. The dimension of the covariance matrix depends only on the number of fixed grid points although each subject may have different numbers of measurements at different time points. The deviance information criterion (DIC) and the Bayesian predictive information criterion (BPIC) are proposed for selecting an optimal number of grid points. To efficiently draw posterior samples, we combine a hybrid Monte Carlo method with a partially collapsed Gibbs (PCG) sampler. We apply the proposed GP model to a mouse dataset on age-related body weight.

• Molecules and Cells
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• 제25권3호
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• pp.417-427
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• 2008

Comparison of maps and QTLs between populations may provide us with a better understanding of molecular maps and the inheritance of traits. We developed and used two reciprocal $BC_1F_1$ populations, IP/DS//IP and IP/DS//DS, for QTL analysis. DS (Dasanbyeo) is a Korean tongil-type cultivar (derived from an indica x japonica cross and similar to indica in its genetic make-up) and IP (Ilpumbyeo) is a Korean japonica cultivar. We constructed two molecular linkage maps corresponding to each backcross population using 196 markers for each map. The length of each chromosome was longer in the IP/DS//IP population than in the IP/DS//DS population, indicating that more recombinants were produced in the IP/DS//IP population. Distorted segregation was observed for 44 and 19 marker loci for the IP/DS//IP and IP/DS//DS populations, respectively; these were mostly skewed in favor of the indica alleles. A total of 36 main effect QTLs (M-QTLs) and 15 digenic epistatic interactions (E-QTLs) were detected for the seven traits investigated. The phenotypic variation explained (PVE) by M-QTLs ranged from 3.4% to 88.2%. Total PVE of the M-QTLs for each trait was significantly higher than that of the E-QTLs. The total number of M-QTLs identified in the IP/DS//IP population was higher than in the IP/DS//DS population. However, the total PVE by the M-QTLs and E-QTLs together for each trait was similar in the two populations, suggesting that the two $BC_1F_1$ populations are equally useful for QTL analysis. Maps and QTLs in the two populations were compared. Eleven new QTLs were identified for SN, SF, GL, and GW in this study, and they will be valuable in marker-assisted selection, particularly for improving grain traits in tongil-type varieties.

• Asian Pacific Journal of Cancer Prevention
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• 제15권18호
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• pp.7955-7958
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• 2014

Breast cancer is the most common cancer among women in the world. In Iran, the incidence of breast cancer is on the increase. We here studied the association of rs1219648 in FGFR2 and rs1042522 in TP53 and their interaction in development of early onset sporadic breast cancer in Iranian Azeri population to evaluate epistatic effects on the risk of mammary neoplasia. We genotyped the two polymorphisms in 100 women with early onset breast cancer and 100 healthy women by PCR-RFLP. Allele frequency differences were tested using $chi^2$-test with 95% confident intervals. Our results indicated a statistically significant association (p<0.05) between rs1219648, but not rs1042522, and risk of breast cancer. We also found that the combination of FGFR2 major genotype and TP53 hetero genotype had protective effects against breast cancer, while the hetero allele of FGFR2 in combination with the minor genotype of TP53 was associated with a high risk. This study revealed an important crosstalk between two polymorphisms in FGFR2 and TP53 in development of breast cancer. These candidates risk variants should be further evaluated in studies with a larger sample size.