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.

Genetic diversity and population structure assessment of Iraqi tomato accessions using fruit characteristics and molecular markers

Rasul Kamaran Salh,Grundler Florian M. W.,Abdul-razzak Tahir Nawroz 한국원예학회 2022 Horticulture, Environment, and Biotechnology Vol.63 No.4

Accessions are a prospective source of genetic variability, as well as valuable genetic resources for crop improvement. Assessing the population structure and genetic diversity of Iraqi tomato accessions is therefore critical in breeding programs for the production of high-yielding cultivars, as well as widening the genetic base of tomato. Using fruit quality indices and molecular markers, a panel of 64 tomato accessions taken from six northern provinces of Iraq were analyzed for genetic diversity and population structure. In the analysis of variance, the fruit phenotypic data revealed a high level of significant variability (p ≤ 0.01) among tomato accessions. The most important characteristics for explaining fruit morphological variability, according to principal component analysis (PCA), were fruit weight, fruit size, fruit diameter, total soluble solids, and moisture content. Seven clades with different fruit characteristics were revealed in the cluster analysis. Genetic diversity and relationships among accessions were analyzed using thirteen inter simple sequence repeat (ISSR), twenty-six start codon-targeted (SCoT) polymorphisms, and fifteen conserved DNA-derived polymorphisms (CDDP). The ISSR, SCoT, and CDDP markers generated 121, 294, and 170 polymorphic bands, respectively, showing a high prevalence of polymorphism. The average polymorphism information content (PIC) values for ISSR, SCoT, and CDDP were 0.81, 0.84, and 0.84, respectively. The accessions were divided into two groups based on the cluster and STRUCTURE analysis results. The Mantel test revealed that three sets of markers had a positive and significant relationship. The increased genetic variation within the populations was found by the analysis of molecular variance (AMOVA), indicating considerable gene exchange between populations. To the best of our knowledge, this is the first extensive report on the use of gene-targeted molecular markers for genetic diversity analysis of tomato accessions in Iraq. Our findings demonstrated the utility of these markers for genetic diversity study in tomato accessions, as well as their potential for genome diversity and germplasm conservation.

Genetic Structure and Composition of Genetic Diversity in the Kouchi Sub-breed of the Japanese Brown Cattle Population

Honda, Takeshi,Fujii, Toshihide,Mukai, Fumio Asian Australasian Association of Animal Productio 2007 Animal Bioscience Vol.20 No.11

Japanese Brown cattle, one of the four domestic beef breeds in Japan, are suffering from numerical reduction due to economic pressure from profitable breeds. In this study, all the reproductive cows in the Kouchi sub-breed of the Japanese Brown cattle that were alive in July 2005 were investigated by pedigree analysis to clarify genetic structure and composition of genetic variability. In addition, genetically important individuals for the maintenance of genetic variability of the sub-breed were also identified through the core set method. The number of cows analyzed was 1,349. Their pedigrees were traced back to ancestors born around 1940, and pedigree records of 13,157 animals were used for the analysis. Principal component analysis was performed on the relationship matrix of the cows, and their factor loadings were plotted on a three-dimensional diagram. According to their spatial positions in the diagram, all the cows were subdivided into five genetically distinctive subpopulations of 131 to 437 animals. Genetic diversity of the whole sub-breed, which is estimated to be 0.901, was decomposed into 0.856 and 0.045 of within-subpopulation and between-subpopulation components. Recalculation of genetic diversity after removal of one or several subpopulations from the five subpopulations suggested that three of them were genetically important for the maintenance of genetic variability of the sub-breed. Applying the core set method to all the cows, maximum attainable genetic diversity was estimated to be 0.949, and optimal genetic contributions assigned to each cow supported the previous results indicating relative importance of the three subpopulations as useful genetic materials.

FGMD : Database of Fungal Genetic Markers and Multigene Analysis in Fungal Classification

Jin-hwa Jang,Se-eun Bae,Sung-hoon Jung,Ha-yeon Kim,In-sung Ahn,Hyeon-seok Son 서울대학교 보건환경연구소 2014 보건학논집 Vol.51 No.2

FGMD (fungal genetic marker database, http://lcbb.snu.ac.kr/fgmd), which contains genetic markers for publicly reported fungal species. The 17 genetic markers used in this study can be used either singly or in combination for the phylogenetic classification of fungi. This database can provide diverse combinations of genetic markers and differs from other databases because it allows for broad systematic analyses based on all species for which sequences are publicly available. We also compared classifications made using single genetic markers to those made using a multigene approach to identify the best combination of markers based on the FGMD for the phylogenetic classification of fungal species. A phylogenetic analysis was performed using 71 species representing four fungal phyla using combinations of three marker genes. Multigene analysis was used for the classification of each species from the species to phylum levels, and error rates for each combination of markers were calculated. Multigene analyses had lower error rates than single-gene analyses. Group prediction by discriminant analysis using multigene markers, which used combinations of Rpb2, Atpase6, and β-Tubulin genes as variables, displayed high accuracy (92%). A multigene approach, such as the one described here, may be applicable as a unified genetic marker for the phylogenetic classification of diverse fungal species.

Evaluating Genetic Diversity of Agaricus bisporus Accessions through Phylogenetic Analysis Using Single-Nucleotide Polymorphism (SNP) Markers

( Youn-lee Oh ),( In-geol Choi ),( Won-sik Kong ),( Kab-yeul Jang ),( Min Ji Oh ),( Ji-hoon Im ) 한국균학회 2021 Mycobiology Vol.49 No.1

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single- nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

Back Analysis of Field Measurements Around the Tunnel with the Application of Genetic Algorithms

김선명,윤지선,전덕찬,윤상길,Kim Sun-Myung,Yoon Ji-Sun,Jun Duk-Chan,Yoon Sang-Gil Korean Geotechnical Society 2004 한국지반공학회논문집 Vol.20 No.7

In this study, the back analysis program was developed by applying the genetic algorithm, one of artificial intelligence fields, to the direct method. The optimization process which has influence on the efficiency of the direct method was modulated with genetic algorithm. On conditions that the displacement computed by forward analysis for a certain rock mass model was the same as the displacement measured at the tunnel section, back analysis was executed to verify the validity of the program. Usefulness of the program was confirmed by comparing relative errors calculated by back analysis, which is carried out under the same rock mass conditions as analysis model of Gens et at (1987), one of back analysis case in the past. We estimated the total displacement occurring by tunnelling with the crown settlement and convergence measured at the working faces in three tunnel sites of Kyungbu Express railway. Those data measured at the working face are used for back analysis as the input data after confidence test. As the results of the back analysis, we comprehended the tendency of tunnel behaviors with comparing the respective deformation characteristics obtained by the measurement at the working face and by back analysis. Also the usefulness and applicability of the back analysis program developed in this study were verified. 본 논문에서는 역해석 방법 중 직접법의 성능에 큰 영향을 미치는 최적화 과정을 인공지능의 한 기법인 유전자알고리즘을 이용하여 역해석 프로그램을 구성하였다. 유전자 알고리즘 및 역해석 기법의 효용성을 검증하기 위하여 과거 역해석 연구 사례 중의 하나인 Gens et al(1987)과 동일한 암반조건을 가진 모델에 대한 역해석을 실시하여 그 결과를 비교${\cdot}$검토하였다. 경부고속철도 터널 현장의 내공변위 및 천단침하에 대한 계측자료로부터 최종 내공변위의 예측함수를 결정하는 방법으로 터널의 총 변위를 분석하였다. 이를 역해석에 필요한 입력자료로 활용하여 역해석을 실시하고 터널 주변 암반의 거동을 반영할 수 있는 지반의 특성치를 구하였다. 각 현장 시험에서 얻어진 지반의 특성치와 비교한 결과 본 연구에서 적용된 유전자 알고리즘을 이용한 역해석 방법이 유의한 수준의 결과를 도출하고 있다는 사실을 확인하였다.

Genetic Diversity and Population Genetic Structure of Black-spotted Pond Frog (Pelophylax nigromaculatus) Distributed in South Korean River Basins

Park, Jun-Kyu,Yoo, Nakyung,Do, Yuno National Institute of Ecology 2021 국립생태원회보(PNIE) Vol.2 No.2

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

Genetic Parameters and Multivariate Analysis to Determine Secondary Traits in Selecting Wheat Mutant Adaptive on Tropical Lowlands

Muh Farid,Nasaruddin Nasaruddin,Yunus Musa,Muhammad Fuad Anshori,Ifayanti Ridwan,Jekvy Hendra,Gatot Subroto 한국육종학회 2020 Plant Breeding and Biotechnology Vol.8 No.4

One of approaches to maintain the yield stability of the lowland tropical wheat is the use of secondary traits in theselection process. The identification of these characters requires a statistical approach in the form of genetic parameter analysis andmultivariate analysis. The objective of this study was to determine the secondary traits of adaptive wheat mutants in the lowlandsthrough the use of genetic parameters and multivariate analysis on the parameters. The study consisted of three field trials conducted inthree different regencies, namely Jeneponto (135 m above sea level (asl)), Maros (100 m asl) and Bantaeng (125 m asl). The study useda nested design, where replications were nested in the environments. The genotype factors consisted of 20 genotypes repeated threetimes. 11 characters were observed including vegetative and reproductive characters. The analysis used consisted of repeatability,correlation, cluster analysis, principal component analysis, factor analysis, and cross print analysis. The overall results of the analysisindicate that the number of productive tillers is the main secondary trait for the selection of adaptive wheat in the lowlands. Thecharacter can be recommended for selection criteria in testing wheat lines in the lowlands to make an effective selection.

Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method

이성영,박태성 한국유전체학회 2018 Genomics & informatics Vol.16 No.4

The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset—namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis. In order to overcome these limitations, we introduce our integration of the PHARAOH method into our recently developed all-in-one workbench. The proposed new PHARAOH program not only supports various de facto standard genetic data formats but also provides many quality control measures and filters based on those measures. We expect that our updated PHARAOH provides advanced accessibility of the pathway-level analysis of large-scale genetic datasets to researchers.

Analysis of the molecular phylogenetics and genetic structure of an invasive alien species, <i>Ricania shantungensis</i>, in Korea

Kwon, Deok Ho,Kim, Se-Jin,Kang, Taek-Jun,Lee, Jang Ho,Kim, Dong Hwan 한국응용곤충학회 2017 Journal of Asia-Pacific Entomology Vol. No.

<P>An invasive alien species, Ricania shantungensis, has been spreading rapidly since it was first reported in Korea in 2010. Molecular phylogenetic analysis using two sets of nuclear and mitochondrial markers showed that the species was well grouped with the genus Ricania while it was clearly distinct from the genus Pochazia. We conducted haplotype analysis using a total of 215 samples collected from six provinces and found that the Korean populations were composed of eight haplotypes. The haplotype and nucleotide diversity of the samples were 0.544 and 0.005, respectively. The 'Hap_1' haplotype occurred at the highest frequency at approximately 65.6%. The genetic distance among the populations ranged from -0.049 to 0.93 and there was no apparent relationship with geographic distance (r(2) = 0.083). The neutrality test detected no rapid population expansion, and a mismatch distribution analysis also supports this finding with a clear multimodal pattern. Instead, severe haplotype decline was detected in almost all of the local populations, which were composed of only 1-3 haplotypes, suggesting the existence of a founder effect. In our UPGMA phylogenetic tree construction, the 12 Korean populations were mainly grouped into four groups that had a significant F-sc value (0.446, P < 0.001) from AMOVA analysis. In summary, genetic difference was not associated with geographical distance and demographic equilibrium was found with severe haplotype decline. Further analysis is needed to trace its origin and dispersal route to establish a management system for invasive alien pests in Korea.</P>