• Genes and Genomics
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• 제40권11호
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• pp.1249-1258
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• 2018

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju${\times}$Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas $r^2$ values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (-0.009) than in Jeju crossbred (-0.035) and Jeju horse (-0.038). $F_{ST}$ value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.202-202
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• 2022

Recently days, soybean production in paddy field is increasing, from 4,422 ha in 2016 to 10,658 ha in 2021 in Korea. It is easy for Phytophthora stem and root rot (PSR) occurring in paddy field condition, when it is poorly drained soils with a high clay content, and temporary flooding and ponding. Therefore PSR resistant soybean cultivar is required. The objective of this study is to identify QTL region and candidate genes relating to PSR resistance of the race in main soybean cultivation area in Korea. 210 soybean materials including cultivars and germplasm were used for inoculation and genome-wide association study (GWAS). Inoculation was conducted using stem-scar method with 2 replications in 2-year for the race 3053 from Kimje and 3617 from Andong. 210 materials were genotyped with Soya SNP 180K chip, and structure analysis and association mapping were conducted with QTLMAX V2. The results of inoculation showed that survival ratio ranged from 0% to 96.7% and mean 9.7% for 3053 and ranged from 0% to 100% and mean 7.6% for 3617. Structure analysis showed linkage disequillibrium (LD) was decayed below r²=0.5 at 335kb of SNP distance. Significant SNPs (LOD>7.0) were identified in Chr 1, 2, 3, 4, 5, 11, 14, 15 for 3053 and Chr 1, 2, 3, 7, 10, 14 for 3617. Especially, LD blocks (AX-90455181;15,056,628bp~AX-90475572;15,298,872bp) in Chr 2 for 3053 and 3067 were duplicated. 29 genes were identified on these genetic regions including Glyma.02gl47000 relating to ribosome recycling factor and defense response to fungus in Soybase.

• Genomics & Informatics
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• 제6권1호
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Journal of Pharmaceutical Investigation
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• 제39권5호
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• pp.345-351
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• 2009

Organic cation transporters (OCTs) are important for absorption, elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is located in a cluster on chromosome 6 and OCTs are in major organs such as intestine, liver, kidney, brain and placenta. Therefore, expression levels and function of OCTs directly affect plasma levels and intracellular concentrations of drugs and thereby determine therapeutic response. The aim of this study was to investigate the frequency of the SNPs on OCT1 (C181T and C1022T) and OCT2 (G808T) to analyze haplotype frequency in healthy Korean population. Human subjects have been genotyped for OCT1 (C181T for 195 subjects and C1022T for 825 subjects), using polymerase chain reaction-based diagnostic tests (RFLP). And for OCT2 (G808T), a total of 861 subjects have been genotyped, using pyrosequencing method. Haplotype was statistically inferred using an algorithm based on the expectation-maximization (EM). OCT1 C181T genotyping showed 100% homozygous wild-type (C/C). OCT1 C1022T genotyping showed wild-type (C/C), heterozygous (C/T) and homozygous mutant-type (T/T) and each accounted for 72.1, 24.5 and 3.4%, respectively. OCT2 G808T genotyping results also showed homozygous wild-type (G/G), heterozygous (G/T) and homozygous mutant-type (T/T) and each took 81.8, 17.9 and 0.3%, respectively. Based on these genotype data, haplotype analysis between OCT1 C181T and OCT1 C1022T has proceeded. The result has revealed that linkage disequilibrium between alleles is not obvious (P=0.0122).

• Journal of Plant Biotechnology
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• 제42권4호
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• pp.290-297
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• 2015

배나무는 원산지와 분화방향에 따라 유럽, 미국, 호주 등에서 주로 재배되는 서양배와 중국, 일본, 한국 등 동남 아시아 지역을 중심으로 분포 및 재배되고 있는 동양배로 구분된다. 17개의 기본염색체를 가진 배나무는 대부분 이배성(2n=2x=34)이며, 단일 S 유전자좌에 의해 조절되는 자가불화합성과 과수 작물의 주요 특징인 유년성으로 인해 유전 연구 및 정밀한 품종 육성에 큰 제한을 받고 있다. 배나무속 식물의 유전연구는 분자생물학 관련 기술의 발달로 다양한 형태의 분자 표지의 개발이 이루어짐과 동시에 유연관계분석, 유전자지도작성, QTL 분석과 같은 다양한 유전연구에 활발히 이용되었다. 또한 배나무의 유전자지도는 병 저항성이나 다양한 유용형질과 연관된 QTL 확인을 위한 연구로 이어지고 있다. 대량 병렬 반응 및 다중처리를 토대로 획기적인 염기서열 분석 비용의 감소를 이뤄낸 NGS 기술은 대용량, 고효율, 저비용으로 식물 유전체 해독을 가능하게 하여, 중국배 'Danshansuli'와 유럽배 'Bartlett'에서 유전체 분석이 완료되었다. 최근 국내에서는 황금배, 청실리 및 미니배의 resequencing 및 GBS를 통한 SNP 탐색 등의 연구를 통해 화기, 숙기 당도 등 농업적으로 유용형질에 대한 게놈전체 연관분석을 수행하고 있다.

• Nutrition Research and Practice
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• 제9권1호
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• pp.79-86
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• 2015

BACKGROUND/OBJECTIVES: It is well-known that alcohol consumption is associated with stroke risk as well as with aldehyde dehydrogenase 2 gene (ALDH2) polymorphisms. However, it is unclear whether ALDH2 polymorphisms are associated with stroke risk independent of alcohol consumption and whether such association is modified by sex. We evaluated sex-specific associations of a common ALDH2 polymorphism and alcohol consumption with stroke risk in a Korean population. SUBJECTS/METHODS: We conducted a prospective cohort study involving 8,465 men and women, aged 40-69 years and free of stroke between June, 2001 and January, 2003, and followed for the development of stroke. We identified new cases of stroke, which were self-reported or ascertained from vital registration data. Based on genome-wide association data, we selected a single-nucleotide polymorphism (rs2074356), which shows high linkage disequilibrium with the functional polymorphism of ALDH2. We conducted Cox proportional hazards regression analysis considering potential risk factors collected from a baseline questionnaire. RESULTS: Over the median follow-up of 8 years, 121 cases of stroke were identified. Carrying the wild-type allele of the ALDH2 polymorphism increased stroke risk among men. The multivariate hazard ratio [95% confidence interval] of stroke was 2.02 [1.03-3.99] for the wild-type allele compared with the mutant alleles, but the association was attenuated after controlling for alcohol consumption. Combinations of the wild-type allele and other risk factors of stroke, such as old age, diabetes mellitus, and habitual snoring, synergistically increased the risk among men. Among women, however, the ALDH2 polymorphism was not associated with stroke risk. CONCLUSIONS: The prospective cohort study showed a significant association between a common ALDH2 polymorphism and stroke risk in Korean men, but not in Korean women, and also demonstrated that men with genetic disadvantages gain more risk when having risk factors of stroke. Thus, these men may need to make more concerted efforts to control modifiable risk factors of stroke.

• Asian Pacific Journal of Cancer Prevention
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• 제15권1호
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• pp.85-91
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• 2014

Background: Genome-wide association studies (GWAS) have identified various genetic susceptibility loci for breast cancer based mainly on European-ancestry populations. Differing linkage disequilibrium patterns exist between European and Asian populations. Methods: Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, rs11878583 in ZNF577, rs7166081 in SMAD3, rs16917302 in ZNF365, rs311499 in 20q13.3, rs1045485 in CASP8, rs12964873 in CDH1 and rs8170 in 19p13.1) were here genotyped in 1009 Chinese females (487 patients with breast cancer and 522 control subjects) using the Sequenom MassARRAY iPLEX platform. Association analysis based on unconditional logistic regression was carried out to determine the odds ratio (OR) and 95% confidence interval (95% CI) for each SNP. Stratification analyses were carried out based on the estrogen receptor (ER) and progesterone receptor (PR) status. Results: Among the 10 SNPs, rs10941679 showed significant association with breast cancer when differences between the case and control groups in this Han Chinese population were compared (30.09% GG, 45.4% GA and 23.7% AA; P = 0.012). Four SNPs (rs311499, rs1045485, rs12964873 and rs8170) showed no polymorphisms in our study. The remaining five SNPs showed no association with breast cancer in the present population. Immunohistochemical tests showed that rs2075555 was associated with ER status; the AA genotype showed greater association with ER negative than ER positive (OR = 0.54, 95% CI, 0.29-0.99; P = 0.046). AA of rs7166081 was also associated with ER status, but showed a greater association with ER positive than negative (OR = 1.59, 95% CI = 1.04-2.44; P = 0.031). However, no significant associations were found among the SNPs and PR status. Conclusion: In this study using a Han Chinese population, rs10941679 was the only SNP associated with breast cancer risk, indicating a difference between European and Chinese populations in susceptibility loci. Therefore, confirmation studies are necessary before utilization of these loci in Chinese.