Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population

Meng Fanbing,Cai Jiancheng,Wang Chunan,Fu Dechang,Di Shengwei,Wang Xibiao,Chang Yang,Xu Chunzhu 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.12

Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigreebased inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between FROH and FSNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix. Conclusion: Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig. Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree.Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm.Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (F_PED) was significantly different from those estimated from runs of homozygosity (F_ROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between F_ROH and F_SNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix.Conclusion: Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig.

Association of the G134A and G184C Polymorphisms in the CYP1A1 Gene with Lung Cancer Incidence

Doug-Young Ryu,Mingai Huang,Changbo Park,Soo Im Chang,Ruth Im,Seong-Jin Choi,Na-Young Kim,In Won Park,Byoung Whui Choi,Jae Yeol Kim,Jong Wook Shin,Jae Chul Choi,Byung-Sun Choi,Jung-Duck Park 한국독성학회 2008 Toxicological Research Vol.24 No.2

The G184C and G134A single nucleotide polymorphisms (SNPs) of the CYP1A1 gene result in Ala62Pro and Gly45Asp substitutions, respectively. Here, we tested whether these SNPs are associated with an alteration in lung cancer incidence. We examined 80 Korean subjects with lung cancer and 240 age- and sex-matched controls. For each subject, the CYP1A1 gene was PCR amplified and sequenced. We observed that the odds ratio (OR) for lung cancer was 3.37 higher in subjects with the G184C polymorphism than in controls (95% confidence interval (CI), 0.89~12.73, P = 0.07). In contrast, the OR for lung cancer was 1.23 in subjects with the G134A polymorphism compared to controls (95% CI, 0.68~2.20, P = 0.49). The G184C polymorphism exacerbated the effects of smoking on lung cancer development. Gene-smoking interaction analyses revealed that past or present smokers with the G184C polymorphism had a higher incidence of lung cancer (OR, 24.72; 95% CI, 4.48~136.31; P < 0.01) than control smokers (OR, 6.65; 95% CI, 2.72~16.28; P < 0.01). However, there was only a slight difference in the ORs for lung cancer between control smokers and smokers with the G134A polymorphism. These findings suggest that the G184C polymorphism, but not the G134A polymorphism, is associated with an increased risk of lung cancer.

Association of the G134A and G184C Polymorphisms in the CYP1A1 Gene with Lung Cancer Incidence

Ryu, Doug-Young,Huang, Ming-Ai,Park, Chang-Bo,Chang, Soo-Im,Im, Ruth,Choi, Seong-Jin,Kim, Na-Young,Park, In-Won,Choi, Byoung-Whui,Kim, Jae-Yeol,Shin, Jong-Wook,Choi, Jae-Chul,Choi, Byung-Sun,Park, Jun Korean Society of ToxicologyKorea Environmental Mu 2008 Toxicological Research Vol.25 No.3

The G184C and G134A single nucleotide polymorphisms(SNPs) of the CYP1A1 gene result in Ala62Pro and Gly45Asp substitutions, respectively. Here, we tested whether these SNPs are associated with an alteration in lung cancer incidence. We examined 80 Korean subjects with lung cancer and 240 age- and sex-matched controls. For each subject, the CYP1A1 gene was PCR amplified and sequenced. We observed that the odds ratio(OR) for lung cancer was 3.37 higher in subjects with the G184C polymorphism than in controls(95% confidence interval(CI), $0.89{\sim}12.73$, P=0.07). In contrast, the OR for lung cancer was 1.23 in subjects with the G134A polymorphism compared to controls(95% CI, $0.68{\sim}2.20$, P=0.49). The G184C polymorphism exacerbated the effects of smoking on lung cancer development. Gene-smoking interaction analyses revealed that past or present smokers with the G184C polymorphism had a higher incidence of lung cancer(OR, 24.72; 95% CI, $4.48{\sim}136.31$; P<0.01) than control smokers(OR, 6.65; 95% CI, $2.72{\sim}16.28$; P<0.01). However, there was only a slight difference in the ORs for lung cancer between control smokers and smokers with the G134A polymorphism. These findings suggest that the G184C polymorphism, but not the G134A polymorphism, is associated with an increased risk of lung cancer.

한국 남성 불임환자에서 Protamine 1과 2 유전자의 Single Nucleotide Polymorphism에 관한 연구

이형송,최혜원,박용석,서주태,궁미경,전진현,Lee, Hyoung-Song,Choi, Hye Won,Park, Yong-Seog,Seo, Ju Tae,Koong, Mi Kyoung,Jun, Jin Hyun 대한생식의학회 2005 Clinical and Experimental Reproductive Medicine Vol.32 No.3

Objective: Although several genetic factors have been associated with defects in human spermatogenesis, the unambiguous causative genes have not been elucidated. The male infertility by haploinsufficiency of PRM1 or PRM2 has been reported in mouse model. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of PRM1 and PRM2, related to the genotype of Korean infertile men. Methods: Genomic DNAs were extracted from peripheral bloods of infertile men with oligozoospermia or azoospermia, and analyzed using polymerase chain reaction (PCR) and direct sequencing. We carried out the direct sequencing analysis of amplified fragments in PRM1 (557 nucleotides from -42 to 515) and PRM2 (599 nucleotides from 49 to 648) genes, respectively. Results: Three SNPs of coding region in the PRM1 gene was found in the analysis of 130 infertile men. However, the SNPs at a133g (aa 96.9%, ag 3.1% and gg 0.0%), c160a (cc 99.2%, ca 0.8% and aa 0.0%) and c321a (cc 56.9%, ca 35.4% and aa 7.7%) coded the same amino acids, in terms of silence phenotypes. On the other hand, as results of the PRM2 gene sequencing in 164 infertile men, only two SNPs, g398c (gg 62.2%, gc 31.1% and ga 6.7%) and a473c (aa 63.4%, ac 29.9% and cc 6.7%), were identified in the intron of the PRM2 gene. Conclusions: There was no mutation and significant SNPs on PRM1 and PRM2 gene in Korean infertile men. These results suggest that the PRM1 and PRM2 genes are highly conserved and essential for normal fertility of men.

Genetic predisposition of donors affects the allograft outcome in kidney transplantation: Single-nucleotide polymorphism of aquaporin-11

( Ji In Park ),( Seung Hee Yang ),( Jung Pyo Lee ),( Seong Ho Yoo ),( Yon Su Kim ) 대한신장학회 2015 Kidney Research and Clinical Practice Vol.34 No.1

Background: Aquaporin-11 (AQP11) is a novel member of the aquaporin family. Disruption of the murine Aqp11 gene causes severe proximal tubular injury and renal failure. The rs2276415 (G4A) single-nucleotide polymorphism in the human AQP11 gene results in glycine to serine substitution in a functionally important domain. In this study, the role of the genetic predispositions of AQP11 rs2276415 (G4A) on renal allograft outcomes was evaluated. Methods: A total of 198 pairs of donors and recipients were enrolled in this study. Long-term graft survival was traced and clinical parameters that could have in.uenced graft outcome were collected through the electronic medical record system. Results: The genotype distribution and allele frequency of rs2276415 polymorphism were not different between donors and recipients. Despite similar allele frequencies between donors and recipients, the minor allele rs2276415 (GAþAA) of AQP11 from the donors, but not from the recipients, had a harmful effect on the graft survival compared with the wild-type donor (GG; P¼0.029). This associationwas signi.cant after adjusting for several risk factors including age, sex, human leukocyte antigen mismatch, donor type, hypertension, and diabetes mellitus (P¼0.032). Conclusion: A donor-derived, not recipient-derived, genetic AQP11 polymorphism has different effects on graft outcome. Thus, the genetic in.uence from donors should be carefully considered for proper management of allografts after kidney transplantation. Copyright & 2015. The Korean Society of Nephrology. Published by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Transcriptome Characterization and Single Nucleotide Polymorphism (SNP) Identification in Vicia amurensis Oett. Using Next-Generation Sequencing Technology

( Suresh Sundan ),( Tae Sung Kim ),( Sebastin Raveendar ),( Gyu Taek Cho ),( Jung Sook Sung ),( Yong Gu Cho ),( Sok Young Lee ),( Kyung Ho Ma ),( Jong Wook Chung ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.3

Vicia amurensis is a perennial plant found in Northern China, Japan, and Korea that plays an important role in sustainable agricultural practices due to its ability to fix atmospheric nitrogen in a symbiotic association with rhizobia. 454 sequencing technology was used to sequence the V. amurensis transcriptome which yielded 26.41 Mb from 71,197 reads as a result of 24,959 valid singletons. In addition, 1743 contigs, with the largest contig size being 3534, and 26,702 unigenes were detected. The contig distributions in three non-mutually exclusive Gene Ontology classifications and clusters of orthologous gene classes showed that differentially expressed genes were generally overrepresented in general function and prediction alone (176, 14.47%), and posttranslational modifications, protein turnover, chaperones (162, 13.32%). In total, 12,656 single nucleotide polymorphism (SNP) types were detected; these variants contained 10,585 SNPs, 1513 indels and 558 variants involving more than one nucleotide. The 2383 SNP types with high confidence differences were identified. The present study provides invaluable information on the functional genomic resources and future biological research on V. amurensis. The SNPs identified in this study will provide a material basis for future mapping and marker-assisted breeding analyses.

Construction and Expression of Mutant cDNAs Responsible for Genetic Polymorphism in Aldehyde Oxidase in Donryu Strain Rats

Adachi, Mayuko,Itoh, Kunio,Masubuchi, Akiko,Watanabe, Nobuaki,Tanaka, Yorihisa Korean Society for Biochemistry and Molecular Biol 2007 Journal of biochemistry and molecular biology Vol.40 No.6

We demonstrated the genetic polymorphism of aldehyde oxidase (AO) in Donryu strain rats: the ultrarapid metabolizer (UM) with nucleotide mutation of (377G, 2604C) coding for amino acid substitution of (110Gly, 852Val), extensive metabolizer (EM) with (377G/A, 2604C/T) coding for (110Gly/Ser, 852Val/Ala), and poor metabolizer (PM) with (377A, 2604T) coding for (110Ser, 852Ala), respectively. The results suggested that 377G > A and/or 2604C > T should be responsible for the genetic polymorphism. In this study, we constructed an E. coli expression system of four types of AO cDNA including Mut-1 with (377G, 2604T) and Mut-2 with (377A, 2604C) as well as naturally existing nucleotide sequences of UM and PM in order to clarify which one is responsible for the polymorphism. Mut-1 and Mut-2 showed almost the same high and low activity as that of the UM and PM groups, respectively. Thus, the expression study of mutant AO cDNA directly revealed that the nucleotide substitution of 377G > A, but not that of 2604C > T, will play a critical role in the genetic polymorphism of AO in Donryu strain rats. The reason amino acid substitution will cause genetic polymorphism in AO activity was discussed.

Development of a single-nucleotide-polymorphism marker for specific authentication of Korean ginseng (Panax ginseng Meyer) new cultivar "G-1"

Yang, Dong-Uk,Kim, Min-Kyeoung,Mohanan, Padmanaban,Mathiyalagan, Ramya,Seo, Kwang-Hoon,Kwon, Woo-Saeng,Yang, Deok-Chun The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.1

Background: Korean ginseng (Panax ginseng) is a well-known medicinal plant of Oriental medicine that is still in practice today. Until now, a total of 11 Korean ginseng cultivars with unique features to Korean ginseng have been developed based on the pure-line-selection method. Among them, a new cultivar namely G-1 with different agricultural traits related to yield and content of ginsenosides, was developed in 2012. Methods: The aim of this study was to distinguish the new ginseng cultivar G-1 by identifying the unique single-nucleotide polymorphism (SNP) at its 45S ribosomal DNA and Panax quinquefolius region than other Korean ginseng cultivars using multiplex amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR). Results: A SNP at position of 45S ribosomal DNA region between G-1, P. quinquefolius, and the other Korean ginseng cultivars was identified. By designing modified allele-specific primers based on this site, we could specifically identified G-1 and P. quinquefolius via multiplex PCR. The unique primer for the SNP yielded an amplicon of size 449 bp in G-1 cultivar and P. quinquefolius. This study presents an effective method for the genetic identification of the G-1 cultivar and P. quinquefolius. Conclusion: The results from our study shows that this SNP-based approach to identify the G-1 cultivar will be a good way to distinguish accurately the G-1 cultivar and P. quinquefolius from other Korean ginseng cultivars using a SNP at 45S ribosomal DNA region.

The first association study of single-nucleotide polymorphisms (SNPs) of the IFITM1 gene with influenza H1N1 2009 pandemic virus infection

Kim Yong-Chan,원세영,정병훈 대한독성 유전단백체 학회 2021 Molecular & cellular toxicology Vol.17 No.2

Background The interferon-induced transmembrane (IFITM) protein family consists of interferon-stimulated genes (ISGs) that show potent antiviral capacity against a broad range of viruses. Many studies have been performed to investigate an association between IFITM3 polymorphisms and pandemic influenza A 2009 H1N1 virus infection. However, an association study of IFITM1 polymorphisms with susceptibility to this infection has not been reported thus far. Objective To identify an association between the susceptibility to pandemic influenza A 2009 H1N1 virus infection and IFITM1 polymorphisms, we compared genotype, allele and haplotype frequencies of the IFITM1 gene between healthy controls and pandemic influenza A 2009 H1N1-infected patients. In addition, we investigated linkage disequilibrium (LD) by Haploview 4.2 and the binding ability of transcription factors according to IFITM1 polymorphism alleles by PROMO. Furthermore, we measured the LD value between the IFITM1 gene and the IFITM3 gene. Results We found 3 novel single-nucleotide polymorphisms (SNPs) and did not find an association between IFITM1 SNPs and susceptibility to pandemic influenza A 2009 H1N1 virus infection. We found strong LD among IFITM1 SNPs but did not find a difference in the transcription factor-binding ability according to regulatory IFITM1 SNP alleles. In addition, we found strong LD between IFITM1 SNPs and IFITM3 SNPs. Conclusion To the best of our knowledge, this report is the first association study of the susceptibility to pandemic influenza A 2009 H1N1 virus infection and IFITM1 polymorphisms. Background The interferon-induced transmembrane (IFITM) protein family consists of interferon-stimulated genes (ISGs) that show potent antiviral capacity against a broad range of viruses. Many studies have been performed to investigate an association between IFITM3 polymorphisms and pandemic influenza A 2009 H1N1 virus infection. However, an association study of IFITM1 polymorphisms with susceptibility to this infection has not been reported thus far. Objective To identify an association between the susceptibility to pandemic influenza A 2009 H1N1 virus infection and IFITM1 polymorphisms, we compared genotype, allele and haplotype frequencies of the IFITM1 gene between healthy controls and pandemic influenza A 2009 H1N1-infected patients. In addition, we investigated linkage disequilibrium (LD) by Haploview 4.2 and the binding ability of transcription factors according to IFITM1 polymorphism alleles by PROMO. Furthermore, we measured the LD value between the IFITM1 gene and the IFITM3 gene. Results We found 3 novel single-nucleotide polymorphisms (SNPs) and did not find an association between IFITM1 SNPs and susceptibility to pandemic influenza A 2009 H1N1 virus infection. We found strong LD among IFITM1 SNPs but did not find a difference in the transcription factor-binding ability according to regulatory IFITM1 SNP alleles. In addition, we found strong LD between IFITM1 SNPs and IFITM3 SNPs. Conclusion To the best of our knowledge, this report is the first association study of the susceptibility to pandemic influenza A 2009 H1N1 virus infection and IFITM1 polymorphisms.

SNPs and Haplotypes of Ets variant 6 (ETV6) Gene Is Associated with Overweight/Obese in Korean Population

Kyung Hee Jung,Sung Wook Kang,Su Kang Kim,Jeong Yoon Song,Hyung Kyung Park,Hyung Hwan Baik 대한스트레스학회 2009 스트레스硏究 Vol.17 No.2

Ets variant 6 (ETV6) 유전자는 염색체의 재배열과 관련이 있는 백혈병에 관련이 되었다고 알려져 있다. 이번 연구에서, 과체중이 백혈병과 과체중/비만에 위험 요소로 작용을 조사하였다. 55개의 single nucleotide polymorphisms (SNPs)을 Affymetrix Genotyping chip array 방식을 이용 분석하였는데, 분석에는 206명의 과체중/비만과 152명의 한국 정상인이 참여되었다. 그리고 통계분석으로는 logistic and multiple regression 방법이 사용되었다. 55개의 polymorphism 중, 4개 (rs2723825, rs17818048, rs2710304 그리고 rs7296981)에서 유의성이 관찰되었다. 그리고 2개의 하플로 타입 중에 블록 7(GGG)과 9(CCC)에서 유의성이 있는 확인할 수 있었다. 유의성을 보였던 블록에는 유의성이 있던 polymorphism이 포함되어 있었다. 우리의 실험 결과에서, ETV6는 한국인의 과체중/비만에 관계가 있다는 것을 밝혀졌다. Ets variant 6 (ETV6) gene is known to be involved in a large number of chromosomal rearrangements associated with leukemia. In recent study, it is reported that excess body weight may be a risk factor for leukemia and overweight/obesity have greater risk of leukemia compared to non-overweight individuals. For a possible relation of the genetic polymorphism of ETV6 with overweight/obesity, we genotyped fifty-five single nucleotide polymorphisms (SNPs) of ETV6 using the Affymetrix Genotyping chip array in 206 overweight/obese and 152 normal subjects in the Korean population. Logistic and multiple regression models were employed to analyze the genetic contributions of polymorphisms. Of the fifty five polymorphisms, the four SNPs showed a significant association with overweight/obesity in 3 alternative models (codominant, dominant, and recessive models; p<0.05 after adjusting for age and sex) were rs2723825, rs17818048, rs2710304, and rs7296981. Two haplotypes of ETV6 (block 7: GGG; block 9: CCC) containing significant polymorphisms (rs17818048, rs2710304, and rs7296981) exhibited significant association with the risk of overweight/obesity. Our results suggest that polymorphisms in ETV6 may be associated with overweight/obese in Korean population. (Korean J Str Res 2009;17:163∼168)