Meta-analysis of Association Studies of CYP1A1 Genetic Polymorphisms with Digestive Tract Cancers Susceptibility in Chinese

Liu, Chang,Jiang, Zheng,Deng, Qian-xi,Zhao, Ya-nan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.11

Background: A great number of studies have shown that cytochrome P450 1A1 (CYP1A1) genetic polymorphisms, CYP1A1 Msp I and CYP1A1 Ile/Val, might be risk factors for digestive tract cancers, including esophageal cancer (EC), gastric cancer (GC), hepatic carcinoma (HC), as well as colorectal cancer (CC), but the results are controversial. In this study, a meta-analysis of this literature aimed to clarify associations of CYP1A1 genetic polymorphisms with digestive tract cancers susceptibility in Chinese populations. Materials and Methods: Eligible case-control studies published until December 2013 were retrieved by systematic literature searches from PubMed, Embase, CBM, CNKI and other Chinese databases by two investigators independently. The associated literature was acquired through deliberate search and selection based on established inclusion criteria. Fixed-effects or random-effects models were used to estimate odds ratios (ORs and 95%CIs). The meta-analysis was conducted using Review Manager 5.2 and Stata 12.0 softwares with stability evaluated by both stratified and sensitivity analyses. Moreover, sensitivity analysis and publication bias diagnostics confirmed the reliability and stability. Results: Eighteen case-control studies with 1,747 cases and 2,923 controls were selected for CYP1A1 MspI polymorphisms, and twenty case-control studies with 3, 790 cases and 4, 907 controls for the CYP1A1 Ile/Val polymorphisms. Correlation associations between CYP1A1 Ile/Val polymorphisms and digestive tract cancers susceptibility were observed in four genetic models in the meta-analysis (GG vs AA:OR= 2.03, 95%CI =1.52- 2.72; AG vs AA: OR=1.26, 95%CI =1.07-1.48; [GG+AG vs AA] :OR =1.42, 95%CI=1.20-1.68, [GG vs AA+AG]:OR=1.80, 95%CI =1.40-2.31). There was no association between CYP1A1 Msp I polymorphisms and digestive tract cancers risk. Subgroup analysis for tumor type showed a significant association of CYP1A1 Ile/Val genetic polymorphisms with EC in China. However, available data collected by the study failed to reveal remarkable associations of GC or HC with CYP1A1 Ile/Val genetic polymorphisms and EC, GC or CC with CYP1A1 MspI genetic polymorphisms. Conclusions: Our results indicated that CYP1A1 Ile/Val genetic polymorphisms, but not CYP1A1 Msp I polymorphisms, are associated with an increased digestive tract cancers risk in Chinese populations. Additional well-designed studies, with larger sample size, focusing on different ethnicities and cancer types are now warranted to validate this finding.

Effects of genetic polymorphisms of apolipoprotein A1 on serum HDL cholesterol level in postmenopausal Korean women

Jang-Soo Hong, Sang-Yong Eom, Yong-Dae Kim, Heon Kim 충북대학교 동물의학연구소 2013 Journal of Biomedical and Translational Research Vol.14 No.2

Apolipoprotein A1 (ApoA1) is the major protein component of high density lipoprotein (HDL) cholesterol in blood, and ApoA1 genetic polymorphisms modulate the blood lipid profiles. This study was conducted in order to investigate the association between three genetic polymorphisms (rs670, rs5069, and rs5070) of ApoA1 and blood lipid profiles in postmenopausal Korean women. A total of 130 postmenopausal women who visited a hospital in order to undergo screening tests were subjects of this study. Genetic polymporphisms and blood lipid profiles were determined using a direct sequencing and spectrophotometric assay, respectively. A significant linkage disequilibrium was observed between all tested single nucleotide polymorphisms. ApoA1 rs5070 genetic polymorphism showed a marginally significant association with HDL cholesterol levels (p=0.066). After adjusting for age, body mass index, smoking, alcohol drinking, medication, hypertension, and diabetes mellitus, we found that the ApoA1 rs5070 genetic polymorphism is a significant determinant of HDL cholesterol levels (β=4.421, p=0.037). According to the results of this study, ApoA1 rs5070 genetic polymorphism may be an important genetic marker associated with HDL cholesterol in postmenopausal Korean women.

Effects of genetic polymorphisms of apolipoprotein A1 on serum HDL cholesterol level in postmenopausal Korean women

엄상용,김용대,김헌,홍장수 충북대학교 동물의학연구소 2013 Journal of Biomedical and Translational Research Vol.14 No.2

Apolipoprotein A1 (ApoA1) is the major protein component of high density lipoprotein (HDL) cholesterol in blood, and ApoA1 genetic polymorphisms modulate the blood lipid profiles. This study was conducted in order to investigate the association between three genetic polymorphisms (rs670, rs5069, and rs5070) of ApoA1 and blood lipid profiles in postmenopausal Korean women. A total of 130 postmenopausal women who visited a hospital in order to undergo screening tests were subjects of this study. Genetic polymporphisms and blood lipid profiles were determined using a direct sequencing and spectrophotometric assay, respectively. A significant linkage disequilibrium was observed between all tested single nucleotide polymorphisms. ApoA1 rs5070 genetic polymorphism showed a marginally significant association with HDL cholesterol levels (p=0.066). After adjusting for age, body mass index, smoking, alcohol drinking, medication, hypertension, and diabetes mellitus, we found that the ApoA1 rs5070 genetic polymorphism is a significant determinant of HDL cholesterol levels (β=4.421, p=0.037). According to the results of this study, ApoA1 rs5070 genetic polymorphism may be an important genetic marker associated with HDL cholesterol in postmenopausal Korean women.

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

Liu, Bin,Shen, Linyuan,Guo, Zhixian,Gan, Mailing,Chen, Ying,Yang, Runling,Niu, Lili,Jiang, Dongmei,Zhong, Zhijun,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.7

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

RAPD Markers Revealed Intra and Inter-Population Genetic Diversity of Some Iranian Populations of Bunium persicum (Boiss.) B. Fedtsch.

Maryam Pezhmanmehr,Mohammad Esmail Hassani,Mohammad Fakhre Tabatabaie,Javad Hadian 한국원예학회 2009 Horticulture, Environment, and Biotechnology Vol.50 No.2

In this study, genetic diversities of 24 populations were evaluated and of 6 selected populations of Black cummin (Bunium persicum (Boiss.) B. Fedtsch.) were studied using randomly amplified polymorphic DNA (RAPD) markers. Among the 24 populations, 15 selected random primers produced 228 scorable bands of which 196 (86%) bands were polymorphic. Estimation of genetic similarity based on the polymorphic bands ranged from 0.19 to 0.75. A dendrogram was constructed based on Jaccard’s similarity data by applying the UPGMA method. Maximum and minimum similarity were detected between Circh and Jiroft-Darin and between Bam and Sistan-Baluchestan, respectively. In addition, 6 populations of Black cummin from the main growing areas in Iran were selected to study genetic diversity within populations. Application of 15 RAPD primers produced 229 bands with an average of 14.4 bands per primer of which 216 (94%) bands were polymorphic. Genetic diversity within populations was studied with the average of Nei’s gene diversity analysis and Shannon's information index. Based on RAPD data, maximum and minimum genetic diversity were observed within populations of Ghazvin and Esfahan provinces, respectively. Regarding the ratio of effective number of alleles to observed number of alleles within each population, all populations showed equilibrant allelic distribution according to Hardy-Wienberg equilibrium. High Fst index derived by this study showed that investigated populations were completely different with independent evolution. The results generally showed a high level of genetic diversity among and within evaluated Black cummin populations. This research indicated that RAPD technique is an efficient tool for assessing genetic diversity in Black cummin populations. Understanding genetic variability in this valuable species provides information related to domestication and conservation efforts.

연구논문 : 자연과학; RAPD 마커를 이용한 인삼 품종 및 육성계통의 유전적 다양성 분석

방경환 ( Kyong Hwan Bang ),정종욱 ( Jong Wook Chung ),김영창 ( Young Chang Kim ),조익현 ( Ick Hyun Jo ),김장욱 ( Jang Uk Kim ),신미란 ( Mi Ran Shin ),현동윤 ( Dong Yun Hyun ),김동휘 ( Dong Hwi Kim ),차선우 ( Seon Woo Cha ),김기홍 한국국제농업개발학회 2013 韓國國際農業開發學會誌 Vol.25 No.2

RAPD 마커를 이용하여 인삼 품종 및 육성계통의 유전적 다양성 및 유연관계를 분석한 결과는 다음과 같다. Fig.5. Dendrogram of genetic similarity among Korean ginseng cultivars and breeding lines constructed on the data obtained with 25 RAPD primer 1. 총 130개의 primer 중 polymorphism을 나타내는 70개의 primer를 선발하였고, 그 중 재현성이 있으면서 polymorphism 이 높은 25개의 primer를 선발하였다. 증폭된 DNA 단편의 수는 189개이고, PCR 산물은 100 ~ 2,800 bp 범위로 증폭되었다. 2. 각 primer에 의해 증폭된 DNA 단편의 수는 3개 ~ 17개로 다양하였으며, primer 한 개당 평균 7.6개의 DNA 단편이 증폭되었다. OPD19 primer를 이용한 유전분석 결과, 총 5개의 유전양상이 나타났는데, 약 500 ~ 1,300 bp의 증폭산물에서 품종 및 계통 간 유전적 다형성을 나타냈다. 3. 선발된 primer별 대립인자는 최소 1.33에서 최대 2.00의 범위였고, 평균 1.709이었다. primer별 유전적 다양성은 OPD15가 가장 높았고, OPF2가 가장 낮은 값을 나타내었다. 본 연구에서 분석에 이용된 25개의 RAPD primer 중에서 D15, D19, B5, A19등은 인삼 품종과 계통에서 비교적 높은 수의 대립단편과 높은 유전적 다양성 값을 나타내는 primer 였다. 4. 유사도 계수 0.98을 기준으로 24개의 품종 및 계통을 대상으로 군집분석을 수행한 결과, 미국에서 수집 육성된 G04116과 국내 품종인 천풍, 연풍 그리고 국내 육성 계통인 G04009, G04026, G04069, G04084는 그룹을 형성하지 않았고, 17개의 품종 및 계통은 2그룹으로 분류되었다. I 그룹에는 고풍, 금풍과 12계통(85%), II 그룹에 3계통(15%)이 포함되었다. In this study, Random Amplified Polymorphic DNA (RAPD) analyses were used to clarify the genetic polymorphisms among Korean ginseng cultivars and breeding lines and to classify them into distinct genetic groups. Among 130 primers in RAPD analysis, 25 primers were selected as the appropriate identification of genetic characteristics in Korean ginseng cultivars and breeding lines. Twenty-five RAPD loci generated a total of 189 DNA bands. Amplified PCR products were showed the highly reproducible banding patterns at 100 ~ 2,800 bp. The number of amplified bands for each RAPD primers ranged from 3 to 17 with a mean of 7.6 bands. In the case of OPD19 primer, 5 banding patterns were displayed in Korean cultivars and breeding lines. Banding patterns were approximately 500 to 1,300 bp amplicons. The number of alleles for each RAPD locus ranged from 1.33 to 2.00 with a mean of 1.71 alleles. OPD15 and OPF02 primers demonstrated the highest and the lowest genetic polymorphisms, respectively. Cluster analysis based on genetic similarity estimated by RAPD markers classified Korean cultivars and breeding lines into 2 groups. Group I included Gopoong and 11 breeding lines (50%); group II included 3 breeding lines (1.3%). Consequently, the results of ginseng-specific RAPD markers may prove useful for the evaluation of genetic diversity and differentiation of Korean ginseng cultivars and breeding lines.

Genetic Differences and DNA Polymorphisms between the Fleshy Prawn Fenneropenaeus chinensis and Chinese Ditch Prawn Palaemon gravieri

Yoon Jong-Man,Kim Jong-Yeon The Korean Society of Fisheries and Aquatic Scienc 2005 Fisheries and Aquatic Sciences Vol.8 No.3

Genomic DNA samples isolated from Fenneropenaeus chinensis (fleshy prawn; FP) and Palaemon gravieri (Chinese ditch prawn; CDP) collected in the West Sea, off the Korean Peninsula, at Buan, were PCR-amplified repeatedly. The sizes of the DNA fragments generated by seven different primers varied from 50 bp to 1,600 bp. We identified 358 fragments for the FP species and 301 fragments for the CDP species. There were 18 polymorphic fragments (5.03$\%$) for the FP species and 12 (3.99$\%$) for the CDP species. In total, 66 common fragments (average of 9.4 fragments per primer) were observed for the FP species and 44 fragments (average of 6.3 fragments per primer) were observed for the CDP species. The numbers of specific fragments seen for the FP species and CDP species were 38 and 47, respectively. The complexity of the banding patterns varied dramatically between the primers and the two species. In the FP species, a specific fragment of approximately 1,200 bp generated by primer OPB-04 exhibited inter-individual-specific characteristics that were indicative of DNA polymorphisms. Moreover, in the CDP species, a major fragment of approximately 550 bp generated by primer OPB-20 was found to be specific for the CDP. The average bandsharing value between the two prawn species was 0.421$\pm$0.006, and ranged from 0.230 to 0.611. The dendrogram obtained using the data from the seven primers indicated seven genetic clusters: cluster 1, FLESHY 01, 02, 03, and 04; cluster 2, FLESHY 05, 06, and 07; cluster 3, FLESHY 08, 09, 10, and 11; cluster 4, DITCH 13, 14, 16, and 18; cluster 5, DITCH 12, 15, and 17; cluster 6, DITCH 19, 20, and 21; and cluster 7, DITCH 22. The genetic distance between the two prawn species ranged from 0.071 to 0.642. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two prawn species. Using various arbitrary primers, RAPD-PCR may be applied to identify specific/polymorphic markers that are particular to a species and geographic population, and to define genetic diversity, polymorphisms, and similarities among shrimp species.

Morphometric variation, genetic diversity and allelic polymorphism of an underutilised species Thaumatococcus daniellii population in Southwestern Nigeria

Animasaun, David Adedayo,Afeez, Azeez,Adedibu, Peter Adeolu,Akande, Feyisayo Priscilla,Oyedeji, Stephen,Olorunmaiye, Kehinde Stephen The Korean Society of Plant Biotechnology 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.4

Genetic diversity among Thaumatococcus daniellii populations in the southwestern region of Nigeria were assessed using morphometric and molecular markers to determine the population structure and existing genetic relationship for its improvement, conservation and sustainable utilisation. Populations from five locations in each of the six states were used for the study. Morphometric data were collected on folia characters and analysed for variability. Genome DNA was isolated from the plant leaf and amplified by polymerase chain reaction with inter-simple sequence repeat markers (ISSR) to determine the allelic polymorphism, marker effectiveness and genetic relationship of the population. The results showed significant variations in petiole length and leaf dimensions of the populations within and across the states. These morphometric traits are the major parameters that delimit the populations and they correlated significantly at P≤0.05. Analysis of the electrophoregram showed that the ISSR markers are effective for the diversity study. A total of 136 loci were amplified with an average of 7.16 loci per marker, 63.2% of the loci were polymorphic. The Principal Coordinate Analysis revealed that seven factors accounted for 81.6% of the variation and the dendrogram separated the populations into two major groups at a genetic distance of 10 (about 90% similarity) with sub-groups and clusters. Most populations within the state had a high degree of similarity, nonetheless, strong genetic relationship exists among populations from different states. The close relationship between populations across the states suggests a common progenitor, which are likely separated by ecological or geographical isolation mechanisms.

DNA Polymorphism and Assessments of Genetic Relationships in genus Zoysia Based on Simple Sequence Repeat Markers

Man Kyu Huh(허만규) 한국생명과학회 2015 생명과학회지 Vol.25 No.3

한국에서 채집한 잔디속(genus Zoysia) 식물 종의 유전적 변이를 단순 서열 반복(Inter-Simple Sequence Repeat Markers, ISSR) 마커 시스템으로 조사하였다. 8개의 ISSR 시발체를 이용한 중합효소 사슬 증폭반응에서 86개의 분절의 증폭물을 얻었으며 이 중 76(87.1%)개 분절이 다형성을 나타내었다. ISSR 마커 시스템에서 다형성 정보지수(PIC)는 0.848이었다. 다형성 대립유전자좌위의 퍼센트(Pp)는 41.2%에서 44.7%까지 나타내었다. 네이(Nei)의 유전자 다양성(H)은 0.149에서 0.186까지 이며 평균은 0.170이었다. 샤논(Shannon)의 정보 지수(I)의 평균값은 0.250이었다. 대립유전자좌위에 근거하여 전체 변이에서 종 간 차이를 나타내는 변이의 몫(GST)은 0.601였다. 이는 전체변이의 약 60.1%는 종 간에 있음을 의미한다. 따라서 변이의 약 39.9%는 종 내에 있었다. GST에 근거한 유전자 흐름(이동)은 잔디속 간에는 대단히 낮았다(Nm = 0.332). 계통도는 3개의 뚜렷한 분지군으로 분리되었다. 왕잔디(Zoysia macrostachya)와 금잔디(Z. tenuifolia) 분지군, 갯잔디(Z. sinica) 단독 분지군, 잔디(Z .japonica) 단독 분지군이었다. 결론적으로 잔디속 식물에 대한 ISSR 분석은 유전적 변이를 탐지하는데 유용하며, 종을 구분하는 유전자형의 대한 식별력을 주었다. The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (Pp) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (HT) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (HS) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (GST) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on GST, was very low among species of the genus Zoysia (Nm = 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.

Determination of Genetic Divergence Based on DNA Markers Amongst Monosporidial Strains Derived from Fungal Isolates of Karnal Bunt of Wheat

J.M.seneviratne,Atul K. Gupta,Dinesh Pandey,Indu Sharma,Anil Kumar 한국식물병리학회 2009 Plant Pathology Journal Vol.25 No.4

Genetic variation among the base isolates and monosporidial strains derived from these isolates of Tilletia indica- the causal agent of Karnal bunt (KB) in wheat, was analyzed by morphological, growth behaviors and RAPD-ISSR based molecular polymorphism. Genetic make up of fungal cultures vary among each other. The magnitude of variation in KBPN group is less (narrow genetic base) when compared to the other groups KB3, KB9 and JK (broad genetic base) reflecting that variability is a genetically governed process. The generation of new variation with different growth characteristics is not a generalized feature and is totally dependant on the original genetic make-up of the base isolate generating new monosporidial strains. Thus, it can be concluded that monosporidial strains derived from mono-teliosporic isolate, consists of genetically heterogeneous population. The morphological and genetic variability further suggests that the variation in T. indica strains is predominantly derived through the genetic rearrangements through para sexual means.