Association of SNP Marker in IGF-I and MYF5 Candidate Genes with Growth Traits in Korean Cattle

Chung, E.R.,Kim, W.T. Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.8

Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

Genetic Variations of Eight Candidate Genes in Korean Obese Group

Kang, Byung-Youn,Lee, Kang-Oh,Bae, Joon-Seol,Kim, Ki-Tae,Yoon, Moon-Young,Lim, Seok-Rhin,Seo, Sang-Beom,Shin, Jung-Hee,Lee, Chung-Choo Korean Environmental Mutagen Society 2002 한국환경성돌연변이·발암원학회지 Vol.22 No.1

Obesity is a complex metabolic disorder with a strong genetic component. There are many candidate genes for obesity and its related phenotypes. We studied genetic variations between Korean obese and lean groups. Polymorphisms investigated were the Msp I polymorphism of the $\alpha$$_{2A}$-adrenergic receptor ($\alpha$$_{2A}$-AR) gene, the Mnl I polymorphism of the $\alpha$$_2$-adrenergic receptor ($\alpha$$_2$-AR) gene, the BstO I polymorphism of the $\beta$$_3$-adrenergic receptor ($\beta$$_3$-AR) gene, the Pml I polymorphism of the lamin A/C (LMNA) gene, the Hga I polymorphism of the clearance receptor (NPRC) gene, the Msp I polymorphism of the leptin gene, BclI polymorphism of the uncoupling protein 1 (UCPI) gene and the Hha I polymorphism of the fatty acid binding protein 2 (FABP2) gene. Among these genetic markers, Pml I polymorphism at the LMNA gene and Bcl I polymorphism at the UCP1 gene were significantly associated with obesity. However, further studies are required whether thease findings are reproduced in large population, although two polymorphisms might be useful as genetic markers in the ethiology of obesity in Korean population.ion.

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Functional Stay-Green Trait in Rice

( Jung Hyun Lim ),( Nam Chon Paek ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2

Functional stay-green (FSG) delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green (NFSG) retains only leaf greenness without sustaining photosynthetic activity. Retention of chlorophylls and photosynthetic capacity is important for increasing crop yield. We determined the main-effect quantitative trait loci (QTLs) for FSG traits in the japonica rice SNU-SG1 and isolated candidate genes. To identify QTLs influencing FSG, we analyzed eight traits: (1) 1 day after heading-degree of chlorophyll content of flag leaf, (2) 1 day after heading-degree of chlorophyll content of second leaf, (3) 1 day after heading-degree of chlorophyll content of flag and second leaves, (4) 50 day after heading-degree of chlorophyll content of flag leaf, (5) 50 day after heading-degree of chlorophyll content of second leaf, (6) 50 day after heading-degree of chlorophyll content of flag and second leaves, (7) relative decline degree of chlorophyll content of flag and second leaves, and (8) flowering time. We carried out QTL analysis with F7 RIL from a cross of japonica rice ‘SNU-SG1’ and indica rice ‘Milyang23 (M23)’. Using 131 molecular markers, we identified 18 QTLs for the eight traits with a threshold LOD value > 2.8. Sequence analysis identified 16 candidate genes for 10 main-effect QTLs. Of these, we have chosen seven strong candidate genes for the 10 main-effect QTLs. These genetic resources will be useful for breeding high-yielding rice cultivars.

A genome-wide association study of social genetic effects in Landrace pigs

Hong, Joon Ki,Jeong, Yong Dae,Cho, Eun Seok,Choi, Tae Jeong,Kim, Yong Min,Cho, Kyu Ho,Lee, Jae Bong,Lim, Hyun Tae,Lee, Deuk Hwan Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.6

Objective: The genetic effects of an individual on the phenotypes of its social partners, such as its pen mates, are known as social genetic effects. This study aims to identify the candidate genes for social (pen-mates') average daily gain (ADG) in pigs by using the genome-wide association approach. Methods: Social ADG (sADG) was the average ADG of unrelated pen-mates (strangers). We used the phenotype data (16,802 records) after correcting for batch (week), sex, pen, number of strangers (1 to 7 pigs) in the pen, full-sib rate (0% to 80%) within pen, and age at the end of the test. A total of 1,041 pigs from Landrace breeds were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which comprised 61,565 single nucleotide polymorphism (SNP) markers. After quality control, 909 individuals and 39,837 markers remained for sADG in genome-wide association study. Results: We detected five new SNPs, all on chromosome 6, which have not been associated with social ADG or other growth traits to date. One SNP was inside the prostaglandin $F2{\alpha}$ receptor (PTGFR) gene, another SNP was located 22 kb upstream of gene interferon-induced protein 44 (IFI44), and the last three SNPs were between 161 kb and 191 kb upstream of the EGF latrophilin and seven transmembrane domain-containing protein 1 (ELTD1) gene. PTGFR, IFI44, and ELTD1 were never associated with social interaction and social genetic effects in any of the previous studies. Conclusion: The identification of several genomic regions, and candidate genes associated with social genetic effects reported here, could contribute to a better understanding of the genetic basis of interaction traits for ADG. In conclusion, we suggest that the PTGFR, IFI44, and ELTD1 may be used as a molecular marker for sADG, although their functional effect was not defined yet. Thus, it will be of interest to execute association studies in those genes.

Genetic disorder-related candidate gene studies in Hanwoo

Sung Hyun Cho,Nu-Ri Choi,Dongwon Seo,Prabuddha Manjula,Shil Jin,Seung Hwan Lee,Jun Heon Lee 한국동물유전육종학회 2020 한국동물유전육종학회지 Vol.4 No.1

Identification and selection of genetic disorders are very important for breeding strategy and improvement process of livestock. Therefore, selection against the disease-related causative genes and variants is most ideal breeding method to prevent inheritable genetic disorders for future generations. In case of Hanwoo breeding scheme, the standardized identification method for genetic disorders has not yet been established. Therefore, it is necessary to screening investigate basic study for genetic disorders in Hanwoo. The objective of this study was to investigate mutations of four candidate genes, such as Haemophilia A, Chediak-Higashi syndrome (CHS), Spherocytosis, and Xanthinuria Type II to determine the presence of genetic disorders in Hanwoo. A total of 376 Hanwoo samples were screened by PCR-RFLP and KASP assay genotyping method. As the results, fortunately, mutations causing genetic disorders were not identified in the four candidate genes. However, further studies will be needed to investigate more samples and other disease related genes should be monitored for controlling genetic diseases in Hanwoo.

Genetic Variations in Six Candidate Genes for Insulin Resistance in Korean Essential Hypertensives

Bae, Joon-Seol,Kang, Byung-Yong,Kim, Ki-Tae,Shin, Jung-Hee,Lee, Chung-Choo The Korean Society for Integrative Biology 2001 Korean journal of biological sciences Vol.5 No.4

Hypertension is a complex disease with strong genetic influences. Essential hypertension has been shown to be associated with insulin resistance. To clarify the genetic basis of insulin resistance in Hypertension, case-control association studies were performed to examine candidate genes for insulin resistance in hypertension. Polymorphisms investigated were the BstO I polymorphism of the $\beta$3-adrenergic receptor (ADRB3) gene, the Xba I Polymorphism of the glycogen synthase (GSY) gene, the Dde I polymorphism of the protein phosphatase 1 G subuit (PP1G) gene, the BstE II polymorphism of the glucagon receptor (GCG-R) gene, the Pst 1 polymorphism of the insulin (INS) gene and the Acc I polymorphism of the glucokinase (GCK) gene. No significant differences were observed in the distribution of alleles and genotypes of the ADRB3, GSY PP1G, GCG-R, INS, and GCK genes between hypertensive and normotensive groups. Although the frequencies in each of these polymorphisms were not significantly different between essential hypertensive and normotensive individuals, our results may provide additional information for linkage analysis and associative studies of disorders in carbohydrate metabolism or in cardiovascular disease.

Association of the Single Nucleotide Polymorphisms in RUNX1, DYRK1A, and KCNJ15 with Blood Related Traits in Pigs

Lee, Jae-Bong,Yoo, Chae-Kyoung,Park, Hee-Bok,Cho, In-Cheol,Lim, Hyun-Tae Asian Australasian Association of Animal Productio 2016 Animal Bioscience Vol.29 No.12

The aim of this study was to detect positional candidate genes located within the support interval (SI) regions based on the results of red blood cell, mean corpuscular volume (MCV), and mean corpuscular hemoglobin quantitative trait locus (QTL) in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs) located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15-which are reported to be related to the hematological traits and clinical features of Down syndrome-were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an $F_2$ resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the $F_2$ intercross population. Among them, the MCV level was highly significant (nominal $p=9.8{\times}10^{-9}$) in association with the DYRK1A-SNP1 (c.2989 G<A), and explained 4.9% of the phenotypic variance. However, since linkage disequilibrium is quite extensive in an $F_2$ intercross, our approach has limited power to distinguish one particular positional candidate gene from a QTL region.

Construction of Synaptic Neural Network for Genetic Interaction Analysis

Jaeyong Yee,Mira Park 한국자료분석학회 2021 Journal of the Korean Data Analysis Society Vol.23 No.4

Contribution by a single gene to the association with trait may be either independent or through interactions with other genes. Examining all available genes for the main effect should be carried out without the time constraint. However the number of possible interacting combinations would soon become formidably large with the growing number of genes. Therefore it is often coerced to identify a group of candidate genes for the interaction and investigate only within it. Such an identification process should be able to select the group of genes having possibilities to interact with each other. Main effect of each gene should not necessarily be the criterion for the selection. We devised a neural network process that was quite sensitive to the interaction of a particular gene to the remaining ones. Contribution of each gene to the association by the genes as a whole was estimated. Selection was made based on the statistical significance for the existence of such contribution. It was demonstrated that this process might perform reliable candidate gene selection for the interaction even when the selected genes did not show significant main effect, through single scan of each individual gene.

대규모 유전자 발현양상 분석을 통한 저항성 운동수행능력 유전자 발굴

오승렬 ( Seung Lyul Oh ) 한국운동생리학회 2016 운동과학 Vol.25 No.1

PURPOSE: The purpose of this study was to examine changes of gene transcripts following 4- and 8-week resistance exercise training in rat skeletal muscle using large-scale BeadArray containing probe sets for 22,523 genes. METHODS: Forty-eight male Sprague-Dawley rats were enrolled and into control (CON, n=16) and and exercise (resistance training, RT, n=32) groups. After 4- and 8-weeks of resistance exercise, based upon lifting weight of individual rats, RT subsequently was separated into high performance group (H-RT4, n=8; H-RT8, n=8) and low performance group (L-RT4, n=8; L-RT8, n=8). Rats were assigned to RT were trained to climb a 1-m vertical (85 degree incline) ladder with weights secured to their tails, and they performed 1 set of 10 times of 3 days per week for 8 weeks progressively. Skeletal muscle was taken from the flexor halucis longus (FHL) after 4- and 8-weeks exercise. After separating the total RNA of each group, large-scale gene expression was analyzed by BeadArray using Illunina RatRef-12 Expression BeadChip, and qPCR was used to inspect BeadArray data. We selected genes given the criteria that detection p-value of <.01, M-value {M=log2(condition)-log2(reference)} to >1.0, and DiffScore to >30. RESULTS: The expression of 20 genes significantly increased 4 weeks after resistance exercise compared to L-RT4, and the expression of four genes decreased, including genes with unknown functions. At 8 weeks, the expression of one gene significantly increased compared to L-RT8 and that of one decreased. These genes involved in acute phase response (Hp, Ahsg), anti-inflammatory response (Ambp), C21-steroid hormone biosynthesis (Timp1), heme oxidation (Hmox1), muscle development (Myh6), regulation of cell growth (Igfbp1), vitamin D metabolism (Gc), calcium-mediated signaling (Dscr1), gluconeogenesis (Atf3), regulation of transcription (Nr4a3), and learning and memory (Egr1). CONCLUSIONS: This is the first study to use BeadArray to examine the global mRNA expression in rat skeletal muscle after resistance ladder training. We found expression genes of rat skeletal muscle based on the resistance exercise performance level using BeadArray. These results may help to explain previously reported physiological changes of skeletal muscle and suggest new avenues for further investigation.

알코올 의존과 후보 유전자들간의 연관성 연구

정인원,김헌,홍주봉,지경환,이규영 大韓神經精神醫學會 2002 신경정신의학 Vol.41 No.6

연구목적 : 알코올 대사와 중추신경계내의 알코올 작용부위와 관련한 일부 후보유전자들이 알코올 의존과 관련이 있는지를 확인하고자 하였다. 방 법 : DSM-IV로 진단된 알코올 의존 환자 128명과 정상 대조군 128명을 대상으로 후보 유전자들의 다형성을 중합효소 연쇄반응과 제한효소처리법을 이용하여 동정하였다. 여기서 분리된 대립유전자와 유전자형에 따른 빈도의 차이를 유전자별로 각각 비교하였으며, 알코올 의존에 작용하는 서로 다른 유전자들에 의한 영향력을 배제하기 위하여 logistic regression 분석을 적용하였다. 결 과 : 알코올 의존군에서는 ALDH_2 유전자의 NN(wild type)형이 정상대조군에 비하여 유의하게 많았다(chi-square test, p<0.001). logistic regression analysis를 통하여 다른 유전자들에 의한 영향을 보정한 상태에서 ALDH_2가 NN(wild type)인 경우 다른 아형에 비하여 알코올 의존에 대한 odds ratio는 130.312이며 그 신뢰구간은 (17.22, 986.43)이었다. 한편, ASA는 N-glycosylation 부위에 변이형 대립유전자를 갖고 있는 경우(AG or GG)는 wild type에 비하여 알코올 의존에 대한 위험도는 2.344배이며 그 95% 신뢰구간은 (1.128, 4.871)이었다. 결 론 : 알코올 의존과 ALDH_2 유전자간에는 밀접한 연관성이 확인되었다. 또한 다른 유전자들은 개별 연관분석에서 의미있는 연관성이 관찰되지는 않았지만 logistic regression analysis를 통하여 N-glycosylation 부위에 다형성이 있는 ASA 유전자가 알코올 의존과 관련이 있음을 시사하였다. Objectives : This study was to explore the association between alcohol dependence and five candidate genes related to the metabolism of alcohol and the enzymes of the suspected sites in CNS. Methods : The genotype and allele frequencies of five candidate genes in 128 male hospitalized patients who met DSM-IV criteria for alcohol dependence were compared with 128 age-matched healthy male control subjects using polymerase chain reaction and restriction fragment length polymorphism. A logistic regression analysis was applied in order to exclude the reciprocal interactions among five candidate genes. Results : The NN genotype frequency of the ALDH_2 gene was significantly higher in alcoholic patients than in control subjects(chi-square test, p<0.001). No difference in frequency was found in the other four genes. In a logistic regression analysis, the odds ratio for alcohol dependence in the NN genotype of the ALDH_2 gene and AG or GG genotypes of the N glycosylation site on the ASA gene were 130.312(95% confidence interval, 17.22-986.43) and 2.344(95% confidence interval. 1.128-4.871), respectively. Conclusion : The result reiterates the association of the ALDH_2 gene polyporphism and the alcohol dependence. Logistic regression analysis additionally suggested that the N-glycosylation site on the ASA gene was associated with alcohol dependence.